Giant Wednesday skipper Rob Jones had headed Wednesday into a first-half lead, but Dale, under new boss Steve Eyre, had proved a match for Gary Megson's side before summer signing Prutton thundered home a half-clearance midway through the second period.
Former Manchester City youth-team coach Eyre, who replaced Keith Hill in June, saw his side threaten to spoil the party at Hillsborough when summer signing Ashley Grimes curled a fine effort against the post just before the hour mark.
But Wednesday also hit the woodwork - defender Lewis Buxton's second-half header came back off the crossbar - and Megson's side showed they are a much more resilient proposition than last season by refusing to buckle when Dale were in the ascendancy.
Striker Jean-Louis Akpa Akpro's low shot was parried by Wednesday goalkeeper Nicky Weaver and the visitors went even closer to an equaliser in the 58th minute. Midfielder Grimes, a free signing from Millwall, curled a fine 25-yard shot that had Weaver well beaten only to hit the far post.
Wednesday responded and hit the woodwork themselves in the 63rd minute when Buxton headed Chris Sedgwick's corner against the crossbar before Prutton blasted home the game-clinching goal, thundering a half-clearance into the top corner from 20 yards.