Calvin Zola, Peter Pawlett and Josh Magennis took advantage of some poor Thistle defending, as Derek McInnes' younger players stepped up to the mark at Firhill.
The Dons boss was forced into four changes, with key players such as Barry Robson, Willo Flood, Russell Anderson and Niall McGinn missing out.
But there was little evidence of wholesale changes with the visitors taking control on the 12th minute after a full-blooded opening to the game.
Returning from injury, winger Hayes slalomed inside, beating three Thistle defenders before forcing Scott Fox into an excellent save.
From Hayes' resulting corner, the ball was cleared to Michael Hector, who returned it back into the six-yard-box for Zola to nod into the bottom corner of the net.
Zola was crucial in Aberdeen doubling their lead on 20 minutes, dispossessing Gabriel Piccolo and introducing Pawlett, who dispatched home with two Thistle defenders on the line.
Sixty seconds later, more chaotic defending from the Jags allowed former Inverness winger Hayes to sting the palms of Fox.
Aberdeen's four advanced midfielders supported the lone striker Zola well as Thistle struggled to make anything stick up-front through John Baird or Kallum Higginbotham.
But there were signs of improvement from Thistle at the end of the half with Aaron Taylor-Sinclair forcing an excellent save from Jamie Langfield after the ball ricocheted off Andrew Considine.
On the stroke of the interval, James Craigen broke from midfield and teed up Sean Welsh, who shot into the side-netting.
Aberdeen, though, were back on top after the restart with Hayes almost adding a third less than a minute into the half.
Thistle keeper Fox then pulled off a terrific reactive save on 53 minutes to deny the impressive Cammy Smith, who looked a certainty to score from Gregg Wylde's cross.
The holding-force of the Dons midfield, Ryan Jack, was the first name in the book on the hour mark after a series of rash challenges.
Jags boss Alan Archibald played all his cards before 62 minutes with Kris Doolan, Ross Forbes and Isaac Osbourne adding some fresh legs to the game.
But defensive frailties cost the home side again with 20 minutes to go, as Piccolo lost out to the powering run of Magennis, who slammed home from a tight angle under the keeper.
At the other end, Higginbotham showed a rare glimpse of quality, hitting the post, but it was the sizeable Aberdeen support which went home happy with a convincing victory in Glasgow.