Utley, sidelined for the Phillies' first 76 games due to a chronic knee condition, finished with three hits and brought the Citizens Bank Park crowd to its feet by homering in his first at-bat.
Carlos Ruiz followed Utley's blast with one of his own, putting Philadelphia in good standing for its first three-game win streak this month.
But Pittsburgh's offense took advantage of the porous Phillies' bullpen. Michael McKenry homered and drove in four runs, Casey McGehee belted a solo shot and Neil Walker went 3-for-4 with three runs scored and an RBI.
Andrew McCutchen added a two-run homer off Chad Qualls in the eighth after the hosts pulled within a run, sealing a win for starter James McDonald (7-3), who allowed four runs on six hits over 5 2/3 frames.
Philadelphia, out of starting pitching options as a result of Sunday's doubleheader, had six relievers combine to allow 14 hits. Raul Valdes (2-1) was the first on the hill and yielded three runs on two hits and a pair of walks in two innings to take the loss.