Mark Smith walked with one out in the ninth against Pirates reliever Mark Corey (0-1). Wes Helms followed with a single before Eddie Perez flied out. Clayton followed with a deep fly that left fielder Brian Giles chased down, but the ball hit off Giles' glove as Smith scored the winning run.
The Brewers blew a 6-3 lead entering the ninth inning. Giles had an RBI single and Matt Stairs connected for a two-out, two-run homer off Brewers reliever Leo Estrella (5-1).
Estrella's third blown save in sixth chances cost Milwaukee starter Wes Obermueller his first career victory.
Geoff Jenkins homered and had four RBI to lead the Brewers. Reggie Sanders had four hits for Pittsburgh.