Adam Rooney and Kenny McLean scored early in the second half to seal another three points for the unbeaten Dons.
Partick Thistle will look to Rooney's goal and a question over handball.
And also a superb performance from Dons keeper Danny Ward as the Dons moved up to second with a game in hand.
Thistle manager Alan Archibald wielded the axe pre-match with former captain Danny Seabourne, Ryan Stevenson and Kris Doolan among those dropped to the bench.
New Aberdeen signing Ryan McLaughlin's clearance didn't come through in time so his was a watching brief.
The opening 45 minutes will not live long in the memory with Niall McGinn and Hayes having shots easily held by Thistle goalkeeper Tomas Cerny.
Archibald adopted similar tactics when his side picked up what was a crucial point at Pittodrie in a goal-less draw towards the end of last season.
However, he was hit by yet another injury problem as Frederic Frans was substituted before half-time clutching the back of his right leg.
Aberdeen have already proved this campaign that they can react to that kind of hurdle. As recently as last week against Dundee in fact.
And minutes into the second period, they broke the deadlock - albeit in fortuitous fashion.
McLean's powerful effort was heading wide, Rooney controlled it and fired in from a right angle.
However, Thistle's angry reaction spoke volumes for the complaint that Rooney had used a hand to control the ball.
That came after the hosts' best moment as Sean Welsh brought a stunning save out of on-loan Liverpool goalkeeper Ward.
The Dons doubled their lead shortly afterwards; David Goodwillie's effort saved by Cerny with McLean on hand to thump home the rebound.
Thistle had plenty of the ball from that moment on, but their lack of goal threat just now is a big concern for the Maryhill natives.
Derek McInnes' side have a good knack of managing games they lead in and their goals against record will be as pleasing to the Dons' boss as the points tally.
The result leaves Aberdeen with the only 100% top flight record which will go on the line against their nemesis' of last season when Celtic visit Pittodrie in a fortnight.
Source: BBC Sport