Giovinco started off his second season with an 82nd-minute penalty in a 2–0 away win over Supporters' Shield holders New York Red Bulls, on 6 March; he later also set up Marky Delgado's goal in added time. On 16 April, he scored the then-fastest goal in Toronto FC history at 57 seconds in a 1–0 away win over D.C. United, surpassing the previous record holder Reggie Lambe's by one minute and 50 seconds set in 2012. A week later, he scored both goals in a 2–0 win away to the Montreal Impact in the 401 Derby; with these goals, he equalled De Rosario as the club's all-time top scorer in the MLS with 28 goals in 40 appearances. Giovinco was named to the Team of the Week for his performances. On 7 May, Toronto's home opener, he set up rookie Tsubasa Endoh for his first ever MLS goal in a 1–0 win over FC Dallas, at the newly renovated BMO Field. On 14 May, Giovinco overtook De Rosario as the club's outright all-time top scorer in the MLS, scoring two goals and setting up another in a 4–3 home defeat to Canadian rivals Vancouver. On 29 June, Giovinco helped Toronto FC win the Canadian Championship over Vancouver 2–2 on aggregate, winning on away goals, as he scored the only goal in the first leg on 21 June. On 14 July, he won the 2016 Best MLS Player ESPY Award. In July 2016, Giovinco was included in the roster for the 2016 MLS All-Star Game.