A double from Barry Robson - the first of which came from the penalty spot - and efforts by Peter Pawlett and Niall McGinn had the Dons 4-0 in front at the interval against an Inverness side that went into the encounter unbeaten in their previous seven outings.
Caley Thistle, however, staged a comeback after the break, but despite a brace from top scorer Billy Mckay and a late Graeme Shinnie header, it could not prevent them from slipping down to fourth in the Scottish Premiership table, while victory for Aberdeen took them up to third.
The Dons' success, however, was marred slightly by defender Mark Reynolds being carried off with a bad facial injury after a nasty clash of heads with Inverness full-back David Raven.
With injury ruling out Andrew Considine before the trip to the Highland capital and Clark Robertson still sidelined with a knee problem, Aberdeen boss McInnes is potentially facing a defensive headache ahead of the visit of Motherwell.
He said: "Mark had to go to hospital for stitches. It was a blow to lose him against Inverness because he's such a big player for us.
"He's got a nasty gash in the roof of his mouth and also on his face.
"Andrew Considine picked up a knock against St Mirren and even though he managed a bit of training during the week, he wasn't fit enough to play at Inverness.
"We'll see how he is this week, but it looks as though he's got a tear in his calf."
Caley Thistle manager John Hughes also suffered an injury blow with captain Richie Foran sustaining damage to his shoulder after landing awkwardly following an aerial challenge with Dons skipper Russell Anderson.
The Inverness midfielder tried to play on, but was forced to depart just before the interval and he could now be facing a spell out on the sidelines, according to Hughes.
He said: "It looks like Richie has popped his shoulder. He'll be a big miss for us. We will now have to wait and see how long he is going to be out for as I don't know yet."