Luebke (2-1) issued a pair of walks and struck out five, tossing 75 of his 110 pitches for strikes as the Padres notched their first win in a four-game set against the Phils.
It was the second straight strong start for the Padres' left-hander, who lowered his ERA to 2.52 with the victory.
Orlando Hudson drove in a pair of runs, including an RBI triple during a three-run eighth inning that put the game away.
Roy Halladay (3-1) was saddled with his first loss of the season, surrendering a pair runs on five hits over seven innings. He allowed four walks and struck out five.