In 2016, Giovinazzi took part in the Asian Le Mans Series in the LMP2 class alongside Sean Gelael. They entered the final two rounds at Buriram and Sepang, winning both races. Giovinazzi then entered the Silverstone round of the European Le Mans Series alongside Gelael and Mitch Evans for SMP Racing, in which they came 5th.
In the FIA World Endurance Championship, Giovinazzi took part in the 2016 6 Hours of Fuji alongside Gelael and Giedo van der Garde for the Extreme Speed Motorsports team, in which they finished 4th in the LMP2 class. He then took part in the following round in Shanghai alongside Gelael and Tom Blomqvist, finishing 2nd.
On 5 September 2016, it was announced that Giovinazzi would perform simulator work for Scuderia Ferrari. In December, he was confirmed as Ferrari's third driver.