Estrada (3-2) logged his first victory since April 19, limiting the Pirates to three hits. The right-hander issued one walk and struck out five.
Aoki supplied a run-scoring double in the fifth for a 2-0 Brewers lead while Jean Segura added three hits with an RBI as Milwaukee won for just the second time in 11 games.
A.J. Burnett (3-4) was reached for four runs (three earned) on seven hits in a seven-inning effort for the Bucs, who dropped the opener of a four-game series.
Pedro Alvarez got Pittsburgh's only RBI.