Born in Cardiff, Wales, Jacobson signed professional terms with his hometown club in July 2006. He made his league debut as a substitute for Chris Barker in Cardiff's Championship defeat at home to Norwich City on 22 April 2006. He made his first start on 22 August in Cardiff's surprise defeat at home to League Two side Barnet in the Football League Cup, and was voted Man of The Match by the local press.
In November 2006 the Torquay-based newspaper the Herald Express reported that Jacobson was likely to sign for Torquay United on loan, a story backed up by the team's official website. However, the move fell through when Torquay failed to loan Martin Phillips to Exeter City and Torquay chairman Chris Roberts refused to sanction the deal. He joined Accrington Stanley on loan and started their Football League Two match away at Grimsby on 25 November, followed by a Football League Trophy quarter-final tie away at League One club Doncaster Rovers on the following Tuesday.
In February 2007, Jacobson joined Bristol Rovers on loan until the end of the season, and then signed on a permanent basis in the summer of 2007.
Jacobson was the subject of controversy after executing a tackle on Kieron Dyer during a second round Carling Cup match against West Ham United on 28 August 2007. The tackle broke Dyer's tibia and fibula bones in his right leg, rendering him unavailable for both domestic and international selection. West Ham's manager Alan Curbishley, was furious initially accusing Jacobson of conducting himself maliciously, however this was dismissed with a written apology to Jacobson when Curbishley saw the tackle again. Awarded Bristol Rovers Supporters Club Young Player of the Year Award 2007–08. During his spell at Rovers, he was voted Young Player of the Year and helped the team to promotion to League 1 and to the quarter final of the FA Cup, scoring in a penalty shoot out win against Premiership Fulham.
On 8 May 2009, it was announced that Jacobson was to be released by Bristol Rovers at the end of his contract.
On 18 June 2009, Jacobson signed a two-year contract with Oldham Athletic after passing a medical. Jacobson made his long-awaited debut for Oldham on 24 November 2009, playing 45 minutes as a substitute in a 3:nil defeat to Walsall.
In July 2010 he was transfer-listed by the club, along with five other first team players.
On 23 November, he joined Accrington Stanley on loan. On 7 January Stanley announced the loan had been extended until 29 January with an option to extend until the end of the season. The following day he scored his first goal for the club as they beat Bury 1–0. On 31 January 2011 he signed for Stanley on a permanent basis, helping them to achieve a playoff place.
Following the expiration of his Accrington contract,on 28 June 2011 it was announced that he would join Shrewsbury Town on a two-year deal. In an interview he told reporters: "it's the place I wanted to be." Joe made his first appearance for Shrewsbury Town in a 2–0 home win against Crewe Alexandra and scored his first goal as a Shrewsbury player in a 7–2 away win against Northampton Town. In the 2011–12 season he made 45 appearances for Shrewsbury Town in all competitions establishing himself as first-choice left-back with manager Graham Turner. In the 2012–13 season, he was selected as Captain in the absence of Matt Richards as Shrewsbury confirmed their League One status in a 0–0 draw away at Colchester United on 20 April 2013. He retained this role for the final two matches of the season, also scoring in both, against Oldham Athletic and Portsmouth.
By playing an undisclosed amount of matches for Shrewsbury Town, Jacobson triggered a clause in his contract to earn another year, extending his stay to the end of the 2013–14 season. Following Shrewsbury's relegation, Jacobson was released at the end of his contract.
On the 1 July 2014, Jacobson signed a two-year contract with Wycombe Wanderers following his release from Shrewsbury Town.
Since April 2015, Jacobson has scored 3 goals for Wycombe Wanderers with two goals from set pieces.
Jacobson captained the Wales Under-21 side that beat France and Romania until narrowly losing over two legs to England U21 in the 2009 European Championship play-offs in October 2008. John Toshack named him in the senior squad for several friendlies but he is yet to make his debut for the senior team.As of 10 July 2017