The Brewers won their fourth in a row to stay in the chase for the National League's second wild card berth. Milwaukee began the evening 2 1/2 games behind St. Louis for the No. 2 wild card position.
Pittsburgh, which on Aug. 8 was 16 games above the breakeven mark, lost its second straight to fall back to .500.
Estrada (4-6) struck out four and walked one while throwing 96 pitches. Jim Henderson struck out the side in the eighth and John Axford survived a shaky ninth for his 30th save of the season and the 101st of his four-year career.
Estrada also singled in a run in the fifth to give Milwaukee a 2-0 lead and his grounder to shortstop Brock Holt was misplayed for an error in the seventh, allowing another run to score.
Norichika Aoki produced Milwaukee's first run with a homer in the opening inning.
Rookie Kyle McPherson (0-1), who had made seven relief appearances this season, was given his first start and he wound up taking his first major-league loss. McPherson gave up two runs on seven hits in 4 1/3.