Paul Ince's side had led through a neat finish from Ricardo Fuller in the first half, but the former Everton equalised before hitting the bar from the spot late on
The former Everton man had initially equalised after Ricardo Fuller's first half effort at the John Smith's Stadium, but could not complete the turnaround as he smashed his effort from 12 yards against the bar in the final 10 minutes.
Fuller danced through the defence to put Blackpool ahead with his 100th career league goal midway through the first half, after Vaughan had struck narrowly wide for the hosts.
Vaughan thought he had scored on the stroke of half time, only to be denied by a tight offside call.
However, he finally got his side on level terms, latching onto home debutant Duane Holmes' through-ball and lashing an effort past Matt Gilks.
And he was presented with the perfect opportunity to seal a win in the 85th minute after Angel Martinez had tripped Sean Scannell, earning the Spanish midfielder his marching orders for a second bookable offence.
But Vaughan was denied by the woodwork, as Blackpool held on for a precious away point, moving them up to second in the table ahead of the weekend's action.