Juan Uribe hit a two-run homer in the second, and Pablo Osuna had a two-run single in the fourth.
Mark Kotsay homered leading off the fifth, but pinch-hitter Rene Reyes had a sacrifice fly in the sixth and Todd Helton singled in a run in the seventh to make it 6-1.
Scott Elarton (4-4) allowed one run and three hits over six innings, while Ben Howard (1-3) gave up five runs and six hits in 5 1-3 innings.
The Padres closed within one in the ninth when Phil Nevin led off the inning with a home run and after a Kotsay single, Khalil Greene hit his second major league home run, and second in two games. The Padres would not come closer as Brian Fuentes got two outs for his third save in five chances.
Trevor Hoffman pitched a scoreless eighth and has yet to allow a run this season.
Jason Bay, traded to Pittsburgh in a deal that brought Brian Giles west, hit two home runs on Friday night and tallied eight RBI’s.
Bay's eight RBI were the most by a Pirates player since Hall of Famer Ralph Kiner drove in eight against Brooklyn on June 25, 1950. Coming into the game, Bay had two homers and six RBI in 55 career at-bats -- all but eight at-bats with the Pirates. He had one homer and four RBI in his first 17 games with Pittsburgh.
Kit Pellow went 4-for-4 and caught his first major league game. Pellow made his first major league debut on Sept. 11 in St. Louis in left field.
Khalil Greene went 1-4 on the day with two RBI’s on his ninth inning homer.
Humberto Quintero went 1-2 and is hitting .294 as a major leaguer.
Todd Sears went 1-1 and scored on a balk in the eighth.
Denis Savage can be reached at firstname.lastname@example.org