Estrada (6-4) notched his third win in four starts, yielding a lead-off single to Shin-Soo Choo in the first inning. He retired the next 15 consecutive batters en route to the dominating 100-pitch performance.
The right-hander walked two and struck out nine as Milwaukee took the rubber match of a three-game series.
Caleb Gindl smacked a two-run homer and Jean Segura added an RBI to provide the Brewers' offense.
Cincinnati's Greg Reynolds (0-2) absorbed the loss, surrendering two runs on five hits over six innings.
Joey Votto homered for the Reds, who came into the contest trailing National League Central co-leaders Pittsburgh and St. Louis by 2 1/2 games.