It was Milwaukee's 13th win in its last 15 games.
The game was tied at 3-3 when Helms rapped a one-out single off Graves (4-15) in the eighth. Perez followed with a double into the right field corner to drive home Helms.
Luis Vizcaino (4-3) struck out two batters a perfect eighth to pick up the win and Dan Kolb whiffed one in a perfect ninth for his 15th save in 16 opportunities.
Milwaukee scored three times in the first inning against Wilson on a two-run homer by Keith Ginter and an RBI single by Perez.