Crofts' shot from 20 yards bounced agonisingly over keeper Owain fon Williams after appearing to hit a divot on the Edgeley Park surface.
Stockport had created the better of few chances in the first half. David Perkins slid a shot wide early on, then teenager Danny Pilkington tested Brighton keeper Michel Kuipers with a firm, low drive from 15 yards.
Stockport broke the deadlock in the 56th minute when Pilkington curled home from 25 yards after picking up a neat pass from Partridge.
There was still time for Brighton to almost nick a late winner but Nicky Forster wasted the chance.