Nova (10-3) broke a personal three-start winless streak, handling the Bosox on one earned run in a six-inning start. The right-hander issued six hits and a pair of walks while pinpointing 73 of his 111 pitches for strikes.
The Yanks led 3-2 in the fifth inning when Mark Teixeira led off with a single off Jon Lester (5-6) and Alex Rodriguez followed by belting a triple off the wall in Fenway Park's 420-foot, center-field notch.
Bosox outfielder Ryan Sweeney crashed into the wall while chasing the ball, but while shaken up, remained in the game.
Jones later added a two-run homer while Teixeira finished with two hits and an RBI as New York took three victories in its four-game series against Boston.
Lester ended up surrendering five runs (four earned) on nine hits in a 4 1/3-inning effort.
David Ortiz and Mark Aviles produced RBI for the Red Sox.