LeBlanc (3-4) allowed four hits and walked one. The lefty retired the last 14 batters he faced and snapped a four-game losing streak. Luke Gregerson threw a perfect eighth and Heath Bell finished for his 16th save in 19 chances.
Gonzalez lined an opposite-field shot into the flower bed just over the left-field wall to snap a scoreless tie. Scott Hairston connected three pitches later for a 2-0 lead.
Gonzalez drove one into nearly the same spot off Danys Baez in the ninth.
Ryan Howard hit an RBI double with two outs in the ninth, but Bell struck out Jayson Werth to end it. Bell fanned Werth with runners on first and third to preserve San Diego's 6-5 win in 10 innings on Sunday.
The two-time NL champion Phillies are 4-11 since Hamels beat Boston on May 21. Despite a star-studded lineup that's missing Jimmy Rollins, they have scored only 29 runs and been shut out five times in those 15 games.
The NL West-leading Padres won the last two to split a four-game series, improving to 16-11 on the road.
Before Gonzalez and Hairston went deep back-to-back, the Padres didn't even have any hard outs against Hamels. The closest they came to a hit were infield grounders.
Third baseman Placido Polanco charged in and threw out Chase Headley on a broken-bat tapper leading off the fifth. Chris Denorfia and Jerry Hairston Jr. were barely retired on slow rollers to shortstop Wilson Valdez in the sixth.
David Eckstein hit a one-hopper to first baseman Howard leading off the seventh and dived headfirst into the base, but Hamels beat him to the bag.
Hamels was trying to become the second Phillie to throw a no-hitter in less than two weeks. Roy Halladay tossed the 20th perfect game in major league history against Florida on May 29. The Phillies loaded the bases with one out in the first, but Werth grounded into a double play.
