The Green Giants fought back in the bottom half by plating four runs and grabbing a 7-4 lead.
Down to their final out in the ninth, the Clippers got a huge two-run double by Nolan Bryant to tie the game 7-7.
In the 11th inning Muskegon pushed across two runs via walks to gain a 9-7 lead, but the Green Giants scraped together a couple hits and ended the game with a two-r,un walk-off single through the left side of the infield.
Wyatt Featherston led the offense with three hits, while Bryant and Connor Henderson added two apiece.
Mitch Ashcraft went 7 1/3 innings on the mound. allowing six runs, while Brian Taggett threw 2 2/3 innings out of the bullpen, only allowing one run.
The Clippers dropped to 15-19 overall and are in third place in the Great Lakes Summer Collegiate League Northern Division Standings.
Muskegon will look to rebound Saturday night in the finale of the two-game series with the Green Giants.