McGehee, obtained last month in a trade with the Pittsburgh Pirates, socked his first homer as a Yankee in the fourth inning to hand New York a 4-0 advantage.
Nova (11-6) struck out 10 over 7 1/3 innings, limiting Toronto to a pair of runs on five hits and one walk. He had entered the game going 0-5 with an 8.36 ERA in his previous five starts.
Aaron Laffey (3-3) surrendered five runs on seven hits over 5 2/3 innings for the Blue Jays.
Edwin Encarnacion supplied both of Toronto's RBI in the loss.