Jim Gannon's side came back from a goal down to live up to their billing as slight pre-match favourites in a meeting of two sides from Greater Manchester.
Stockport had finished one place and two points above their near neighbours in the final League Two table, but were made to work hard on a wet afternoon at Wembley.
Rochdale had taken the lead in the 24th minute after playing second fiddle for the opening exchanges of a tight encounter.
Chris Dagnall had seen a rising drive deflected for a corner before defender Rory McArdle rose the highest at the near post to direct the resulting flag-kick past a static defence and goalkeeper.
But the early setback appeared to act as a wake-up call for County, who were almost back on level terms five minutes later when Anthony Pilkington's bending 25-yard free-kick whipped just the wrong side of the upright.
The equaliser did come on 34 minutes when the unlucky former Scunthorpe defender Nathan Stanton was unsighted by Jim McNulty from a low Tommy Rowe cross and only succeeded in palming the ball into the back of his own net.
Stockport continued to hold the upper hand and went ahead for the first time in the match on 49 minutes when Pilkington calmly headed a Michael Rose cross which skidded up off the wet surface into the back of the net via the underside of the bar from ten yards.
It looked like game over when the impressive Liam Dickinson - who ran himself into the ground as a lone striker - produced a superb first-time finish to lash a low Pilkington cross between the keeper and his near post to make it 3-1 in the 67th minute.
But Adam Rundle's own tremendous strike when he dispatched an angled volley from the edge of the penalty area past Conrad Logan in the Stockport goal 13 minutes from time set-up a grandstand finish.
However, Stockport held firm and, after losing on each of their four previous visits to Wembley, it was their fans who celebrated a well-deserved promotion at the final whistle.