Luebke (3-1) allowed two runs on seven hits and struck out three.
Huston Street set the Giants down in order in the ninth to get his third save of the year.
Chase Headley scored twice and drove in a run in the Padres' second straight victory.
Eric Hacker (0-1) gave up three runs on eight hits to take the loss in his big league debut. Hacker struck out seven.
Buster Posey had two hits, including a solo home run, and finished with two RBI and one run scored for the Giants, who have lost three of their last four games.
San Francisco's Pablo Sandoval singled in the third to run his franchise-record hitting streak to 20 games.