Sacrifice flies by pinch hitter Mark Loretta and Kazuo Matsui, and Lance Berkman's RBI single, ended the Brewers' shot at winning nine in a row for the first time since taking 10 straight from Aug. 19-28, 2003.
The loss also cost Milwaukee (59-44) a chance at moving into a tie for first with the Chicago Cubs (60-43) in the NL Central. The Cubs lost to the Florida Marlins, 3-2.
Rodriguez (6-3) helped the Astros snap a four-game losing streak in his first start this season against Milwaukee. Houston's last win was his on Saturday, when he held the Cubs to one run in 6 2-3 innings of a 4-1 victory.
Rodriguez also cooled off Ryan Braun, whose two-run homer in the top of the ninth Thursday capped his second straight four-hit game and lifted Milwaukee to a 4-3 victory over the St. Louis Cardinals.
Braun was 0-for-3 with a walk after reaching base in nine straight plate appearances and going 14-for-29 on the Brewers' perfect seven-game trip through San Francisco and St. Louis.
Christopher Sampson pitched 1 1-3 innings of scoreless relief. Wesley Wright retired Prince Fielder, the only batter he faced. Jose Valverde finished for his 26th save in 32 chances as the Brewers' club record of 20 consecutive games with a homer ended.
Milwaukee opened a seven-game homestand with plenty of momentum, but Rodriguez ground them to a halt with his first victory in his last six starts at Miller Park since May 28, 2005.
The Astros chased Manny Parra (9-3) in the seventh and took a 3-1 lead.