After trailing 2-1 entering the bottom of the 8th, the Clippers scratched across a run to tie the game before the Green Giants scored in the top of the ninth to seal the victory.
Muskegon pitcher Bryce Kelley threw seven innings of one-run ball and struck out four, but received a no-decision.
Brian Sobieski led the Clippers offense with three hits, while Nolan Bryant and Jimmy Roche added two apiece.
Muskegon fell to 12-16 on the season, which is good for third place in the Great Lakes Summer Collegiate League Northern Division.
The Clippers will travel to Flat Rock, Michigan on Monday to begin a two-game series with the first-place Lake Erie Monarchs.