Kyle Lafferty and Nikicak Jelavic (penalty) scored in the 58th and 69th minutes respectively to give 'Gers a commanding lead which was cut short when Richard Foster got one back for the Dons with eight minutes remaining.
Rangers remained nine points clear of second-placed Motherwell and pushed 12 ahead of Old Firm rivals Celtic but the gloss was taken off the victory by the knee injury sustained by in-form striker Steven Naismith who had to be stretchered off just after the 20-minute mark.
The Scotland international collapsed unchallenged moments after a collision with Aberdeen's Rob Milsom indicating it could be a similar problem to the one he sustained in 2008 which kept him sidelined for eight months and 'Gers boss Ally McCoist admitted he was worried.
"The signs aren't good. He said it feels similar to when he did his knee before but we won't know until we get a scan and a full diagnosis," he said.
"I would have to say it probably isn't looking good at the moment as he says he feels the same pain and numbness as he did when he did it the first time.
"It's strange because I thought our team played some great stuff in the second half and thoroughly deserved their victory but there is no doubt the shine has been taken off the result by Steven's injury."