Mortara began racing in karts, winning the 2002 South Garda Winter Cup and the 2005 Andrea Margutti Trophy. In 2006 he moved into formula cars with Prema Powerteam, contesting both the Formula Renault Eurocup and Formula Renault 2.0 Italia series.
He joined the Formula 3 Euro Series in 2007 with Signature-Plus, scoring his maiden car racing victory at Brands Hatch and winning the rookie classification. Returning for 2008, Mortara was competitive throughout but faded in the second half of the season, finishing second in the championship behind Nico Hülkenberg and narrowly ahead of Jules Bianchi. He also contested the 2008 Macau Grand Prix, winning the qualification race before finishing second in the main event.
After a stint in GP2 in 2009, Mortara returned to Formula 3 to race at Macau, where he won the main race after passing Jean-Karl Vernay in the closing laps. In 2010 he dominated the Formula 3 Euro Series with Signature, winning seven of the higher-points Saturday races to claim the championship, then completed a Macau double by winning both the qualification race and the main race. He became the first driver ever to win the Macau Grand Prix in consecutive years during the Formula Three era.
Mortara joined Audi Team Rosberg in the Deutsche Tourenwagen Masters for 2011 in the older A4 chassis, scoring his first podium at Brands Hatch and a second at Oschersleben in a wet-affected race. He moved to Audi Sport Team Abt from 2014 and his career reached its peak in 2016.
That year Mortara won the opening race at Hockenheim while ill, then led the championship after his second victory at the Norisring. He added a further win at the Nürburgring and a dominant victory at the Hungaroring, entering the season finale with a 14-point deficit to Marco Wittmann. Mortara recovered to finish third and then won the final race, but Wittmann's fourth place was enough to deny him the title by a narrow margin. Mortara finished second overall in 2016, the closest he came to the DTM championship.
Across his time with Audi in DTM he was a consistent frontrunner, taking his first DTM win at the Red Bull Ring in 2012. He finished fifth in the 2012 standings and was a regular podium contender in subsequent seasons.
Mortara joined the HWA-run Mercedes-AMG Motorsport team for 2017, finishing 14th in the championship with one podium at the Norisring. In 2018 he raised his level significantly, winning at the Lausitzring and the Norisring and finishing sixth in the standings. During his complete DTM career Mortara scored ten race victories, 26 podiums, five pole positions, and six fastest laps.
Alongside his single-seater and DTM work, Mortara established himself as the dominant force at the Macau GT race. He won the Macau GT Cup in 2011, 2012, and 2013, and returned in 2017 to win the FIA GT World Cup in a Mercedes-AMG GT3, his sixth Macau victory overall. His ten Macau wins across F3 and GT categories set a record for any driver at the circuit.
Mortara joined Venturi Racing for the 2017–18 Formula E season and spent six years with the team, which later became Maserati MSG Racing. He scored his first Formula E win at Hong Kong in the 2018–19 season after race winner Sam Bird was penalised. His best championship performances came in 2020–21, when he finished second overall despite a fractured vertebra sustained in a collision at the Berlin finale, and in 2021–22, when he won four races including victories in Diriyah, Berlin, and Marrakesh before finishing third in the standings. He joined Mahindra Racing for the 2023–24 season and continued competing in Formula E into the Gen3 era.
Mortara is recognised as one of the most complete drivers of his generation, equally at home in touring cars, GT machinery, single-seaters, and electric racing. His near-miss in the 2016 DTM title fight, his Macau record, and his two Formula E championship runner-up finishes define a career characterised by speed and versatility across disciplines.