From 2009 to 2011, Nogueira played for the CB Estudiantes junior team. In 2011, he was loaned to CB Las Rozas for the 2011–12 season. In January 2012, he joined CB Estudiantes for the rest of the 2011–12 ACB season, and re-joined the team for the 2012–13 season as well.
On June 27, 2013, the day of the NBA draft, Nogueira signed a two-year contract extension with Estudiantes. He went on to win the ACB's Best Defender award for the 2013–14 season.
On April 17, 2013, Nogueira officially declared for the 2013 NBA draft. Because he had initially decided to declare for the 2011 NBA draft, but ultimately declined to enter it afterwards, Nogueira was not allowed to back out of the 2013 draft. He was selected with the 16th overall pick by the Boston Celtics on behalf of the Dallas Mavericks, who then traded his draft rights to the Atlanta Hawks. In July 2013, Nogueira joined the Hawks for the 2013 NBA Summer League.
On June 30, 2014, Nogueira's draft rights were traded, along with Lou Williams, to the Toronto Raptors in exchange for John Salmons and a 2015 second-round pick. In July 2014, he joined the Raptors for the 2014 NBA Summer League. On August 3, 2014, he signed with the Raptors. On November 21, 2014, he made his NBA debut against the Milwaukee Bucks. In eight minutes of action, he recorded two points, five rebounds and one steal in a 124–83 win. On March 12, 2015, he was assigned to the Fort Wayne Mad Ants of the NBA Development League. He was recalled by the Raptors on March 26, 2015.
In July 2015, Nogueira re-joined the Raptors for the 2015 NBA Summer League. On September 29, 2015, the Raptors exercised their third-year team option on Nogueira's rookie scale contract, extending the contract through the 2016–17 season. On December 5, 2015, he scored a career-high 14 points in a 112–109 loss to the Golden State Warriors. During the 2015–16 season, he had multiple assignments with Raptors 905 of the NBA Development League.
On October 23, 2016, the Raptors exercised their fourth-year team option on Nogueira's rookie scale contract, extending the contract through the 2017–18 season. On November 9, 2016, he scored 10 points on 5-for-5 shooting and had seven rebounds in a 112–102 win over the Oklahoma City Thunder. Three days later, he recorded six points, 10 rebounds, one assist, three steals and a career-high five blocked shots in a 118–107 win over the New York Knicks.
Nogueira played for the Brazilian U-19 national team at the 2011 FIBA Under-19 World Championship. He was fifth in rebounds per game and second in blocks per game.