The Twins have lost three straight after winning eight in a row.
Danny Valencia's three-run homer in the sixth rallied Minnesota into a 3-2 lead but the Brewers came back an inning later.
Milwaukee put runners on first and third against Scott Baker (5-5) and Jose Mijares came on in relief with two away to try to get out of the inning. Fielder, however, hit a 3-2 pitch off Mijares to deep right to bring home both runners.
Milwaukee's Ryan Braun had a ground-rule double in the fifth that drove in a run and extended his career-best hitting streak to 15 games.
Randy Wolf (6-4) gave up the homer to Valencia but got the win by surviving seven innings. He is 3-0 over his last seven starts.
John Axford was perfect in the ninth while picking up his 20th save.