After graduating from the Putney School in 1964, Jones enrolled at Lawrence University as a premed student, where his performances in university productions brought him to the attention of Tyrone Guthrie, who recruited him for the Guthrie Theater in Minneapolis, Minnesota. He then went to London in 1969 to study at the London Academy of Music and Dramatic Art, followed by a three-year stint with the Stratford Theatre in Stratford, Ontario.
His stage career included more than 125 productions, starting with the Guthrie Theater, then internationally in South America, Canada, and London, and ultimately in New York's Broadway theatre, appearing with Sigourney Weaver, Christopher Walken, David Bowie and Meryl Streep. Productions included, Cloud 9, A Flea in Her Ear, Romeo and Juliet and The Elephant Man. His transition from stage to film began in 1970.
Jones began acting in small parts in film and television in the 1970s. In his best-known roles as Emperor Joseph II in Amadeus, Charles Deetz in Beetlejuice, and Edward R. Rooney in Ferris Bueller's Day Off, his dead-pan expression and distinctive face bring a comic flavor to his characters through their reactions to the situations in which they find themselves, more so than the wit in their scripted lines. The New York Times' biographic profile says of Jones, "Although he has tried to steer clear of playing only sinister roles, the actor's imposing height, bugged-out eyes, easy sneer, and shock of reddish-blond hair give him vaguely devilish features that have prompted villain typecasting. However, the actor is also widely respected and considered a boon wherever he appears." The profile describes his portrayals variously as a "hissable, cartoonish high school principal" in Ferris Bueller's Day Off, a "good-natured father" in Beetlejuice, "an interplanetary freedom fighter" in Mom and Dad Save the World, a "demon stand-in" in Stay Tuned, "evil bespectacled twins" in Out on a Limb, plus other personae in a variety of other roles
Jones' roles in Easy Money (1983) and Remington Steele led Miloš Forman to cast him as Emperor Joseph II in Amadeus (1984), an adaptation of the Peter Shaffer play of the same name. According to one reviewer, he portrayed the Emperor "as a superficial and self-absorbed ruler who can't tell the difference between a great opera and a mediocre one". New York Times critic, Vincent Canby, praised Jones' performance as the Emperor, citing the film's most memorable line, when the Emperor complains of The Marriage of Figaro that "there are too many notes". Jones' performance earned him a nomination for the Golden Globe Award for Best Supporting Actor – Motion Picture.
Jones's performance as Edward R. Rooney in the 1986 film, Ferris Bueller's Day Off, made him a cultural icon. Rooney, self-important and obsessed with catching the chronically truant Ferris Bueller, became a symbol of pomposity and authoritarian hatefulness. In a movie review, the New York Times characterized Jones' performance "fine cartoon like ferocity", wherein his character "gets scratched, bitten, attacked by ferocious dogs and covered with mud while pursuing his weaker, but craftier, prey, and emerges each time bruised but undaunted, thinking up some new (and futile) plan." The review likened Jones' role as akin to that of Wile E. Coyote as a character who is fated to be unable to catch The Road Runner (Ferris Bueller). Jones expressed concern about being remembered more for this role than his Emperor Joseph II in 1984's Amadeus. He said of the movie's premise, "What's amazing about Ferris Bueller, is that we're asked to, and do, sympathise with a kid whose only complaint in life is that his sister got a car for her birthday and he got a computer."
In the movie Beetlejuice, Jones played a supporting role, along with Catherine O'Hara, as co-owners of a haunted house. To highlight this couple's status as bores, director Tim Burton casts Dick Cavett and Robert Goulet to appear as their guests at a dinner party, at which the ghosts of the previous owners cause everyone to sing "Day-O (The Banana Boat Song)". Jones went on to act in other films by director Tim Burton, including Ed Wood in the role of The Amazing Criswell, and in the film, Sleepy Hollow.
Jones also appeared in The Hanoi Hilton, The Hunt for Red October, Howard the Duck, "Transylvania 6-5000," Houseguest, The Crucible, The Devil’s Advocate, and Stuart Little. In 1999 he co-starred with Guy Pearce, Robert Carlyle, and David Arquette in the cannibal western Ravenous, and played Inspector Lestrade in Without a Clue. Jones appeared in the comedy film The Pest, as the evil German trying to hunt Pestario "Pest" Vargas. Other key roles include Mr. Spike in Stay Tuned and Dick Nelson in the 1992 comedy Mom and Dad Save the World.
One of Jones's earlier television roles was in an episode of the 1976 CBS series Sara. In 1986, he showcased his villain persona in the role of the sinister Mister Acme (owner of Acme Toxic Waste), in the satirical comedy miniseries Fresno, with Carol Burnett, Charles Grodin and Dabney Coleman. In 1995, Jones co-starred with Tyra Banks, Kathy Najimy, and Kevin Pollak in the video storyline portion of the Walt Disney World Tomorrowland attraction ExtraTERRORestrial Alien Encounter. He also hosted Disneys D-TV Monster Hits musical special, as The Magic Mirror (Snow White). He has had guest roles on a number of television series, including Amazing Stories, Tales from the Crypt, and Batman: The Animated Series. In 1989, he starred in the short-lived CBS sitcom The People Next Door, as a cartoonist whose imagination could make things come to life. He also appeared as newspaper publisher A. W. Merrick on the highly acclaimed HBO series Deadwood.
With ongoing legal troubles, Jones became progressively less active as a performer. Following his appearance in the golf comedy Who's Your Caddy? (2007), he was absent from film and television for several years. He had an uncredited appearance as Collier's editor Charles Colebaugh in the Emmy-nominated HBO original film Hemingway & Gellhorn (2012). His most recent role is that of scientist Gladstone in the disaster film 10.0 Earthquake (2014).
Jones was born in Buffalo, New York, the son of Ruth (née Schooley) and Douglas Bennett Jones. His mother was an art historian, who urged him towards a career in acting. His father died during Jones's childhood.
One interviewer found Jones to value anonymity and the enjoyment of everyday tasks, like home repairs, and found him to be uninterested in status symbols and fan adulation. In that 1989 interview, Jones pointed out that greater public recognition actually makes it more difficult to transition between roles and allow the character to come to the fore and the actor to recede from view.
Jones has one son, actor Julian Coutts, whose mother was Lloy Coutts (1941–2008). Coutts was a respected Canadian voice coach. She and Jones met in Stratford, Ontario.
In 2002, Jones was arrested for possession of child pornography and accused of soliciting a 14-year-old boy to pose for nude photographs. Jones pleaded no contest to a felony charge. His attorney emphasized that there was no allegation of improper physical contact. His punishment was five years probation, counseling, and the requirement to register as a sex offender. In 2010, he was arrested twice for failing to update his sex offender status, both in Florida and in California.