Rodriguez (10-12) struck out six and walked one. His lone mistake came in the sixth inning, when Chase Utley doubled home Jimmy Rollins.
Carlos Lee hit an RBI double in the first and added a solo home run off Philadelphia starter Kyle Kendrick (8-7) in the third. Kendrick, a Houston native who was celebrating his 26th birthday on Thursday, gave up four runs and nine hits in six full frames.
The last time Houston swept the Phillies in a four-game series in Philadelphia was September 6-9, 1999 at Veterans Stadium.
It was another shoddy offensive performance by the Phillies, who have now been held to two runs or fewer in seven of their last eight games.
“We’re having trouble. We’ve been inconsistent all year, but now we’re having trouble generating runs,” Phillies manager Charlie Manuel said of his team’s offense.
The loss dropped Philadelphia out of first place and a half-game behind idle San Francisco in the race for the National League Wild Card and three games back of first-place Atlanta in the NL East. The Braves were also off Thursday.
Already ahead 1-0, former Phillie Michael Bourn pushed home a run with a two- out single in the second. Rodriguez extended the lead to 4-0 in the fourth when his hit plated Angel Sanchez, who led off with a double.
Jayson Werth opened the fifth with a single for the first Phillies hit off Rodriguez and Raul Ibanez followed with a double to put runners on second and third with no out.
In a sequence befitting the Phillies’ recent play at the plate, Shane Victorino struck out and Brian Schneider flied into a 9-2 double play to end the inning.
Utley’s double cut the deficit to 4-1, but the speed of Bourn restored a four- run cushion. J.C. Romero replaced Kendrick to begin the seventh and Bourn reached on an infield single with two outs. After Bourn swiped second, Anderson Hernandez hit a slow roller down the third-base line. Placido Polanco fielded the ball and Hernandez was safe on an infield single. Bourn, though, kept going after reaching third and beat first baseman Ryan Howard’s throw to the plate.
Houston has won five games in a row…The Phillies went 4-6 on their 10-game homestand…Ibanez was 3-for-3 with a walk…Philadelphia had won each of its last eight day games…Bourn had three hits…Houston first baseman Brett Wallace celebrated his 24th birthday…The Astros are 16-7 all-time at Citizens Bank Park, the best record by a visiting NL club…Prior to the game, the Phillies held a ceremony honoring Roy Halladay’s perfect game against the Marlins on May 29 in Florida…Rodriguez has 61 wins in an Astros uniform, tying him with Jim Deshaies for third-most in franchise history…Howard went 1-for-16 and struck out 10 times during the series.