With a point apiece looking the likely outcome, substitute Vernon turned and shot from the edge of the box to give visiting keeper Dean Brill no chance in the 80th minute.
The strike was tough on Brill who had earlier pulled off some fine saves to preserve the visitors' interest in a tense match at Pittodrie.
A crowd of 11,251 saw him at his best in the 18th minute when he denied Cammy Smith with a stunning stop after he had been set up by Calvin Zola.
And the on-loan Luton keeper was called into action soon after when he diverted a Michael Hector header over his bar from a 37th-minute Jonny Hayes corner.
The Dons continued to push for the opener after the break and Hector, Joe Shaughnessy and Peter Pawlett all saw good chances go begging.
Home boss Derek McInnes sent on Josh Magennis for Zola in the 65th minute and within 60 seconds Smith fired the best chance of the game just wide of Brill's goal.
Graeme Shinnie came closest for the visitors with a header in the 69th minute but just 11 minutes later Vernon, who had only been on the park for three minutes after replacing Smith, sent the home crowd into raptures.
The goal sparked life into Caley who were denied a late leveller when Mark Reynolds thwarted Richie Foran with a timely interception deep into time added on.