Commons beat off Celtic team-mates Fraser Forster and Virgil van Dijk, as well as Kilmarnock striker Kris Boyd, for the PFA Scotland Premiership player of the year award.
Midfielder Commons has enjoyed a prolific season, netting 28 goals across all competitions and guiding his team to the Scottish Premiership title.
Dundee United's left-back Andy Robertson was voted young player of the year.
McInnes, who guided the Dons to their first piece of silverware with the League Cup final win over Inverness in March, said: "It is testament to the effort of the players, it shows what can be done with a hungry group of talented boys.
"My assistant manager Tony Docherty has been invaluable to me, and the rest of my staff, so the award is as much for them as for me."
McInnes, whose side are second in the Scottish Premiership, four points ahead of Motherwell with three games remaining, continued: "It is nice to see Aberdeen as a club in a positive light.
"I was at an awards dinner last season and we hardly got a mention and it made me really aware that there was a lot of work to be done. We have had a lot of awards this year, a lot of plaudits so I think that shows how where we have come from as a club and hopefully this time next year there will be something similar again.
"The cup win was needed by the club and the city, the players have enjoyed that success and I think that has whetted their appetite to be successful in the cups again. We can't be satisfied with that we have done, I would like to think there is still more to come from us.
"We are not obsessed with finishing second, we just wanted to make sure we improved but now that we are here, with three games to go we want to secure European football.
"Hopefully we can get the points to get European football and if we can move
on to second then so be it."
Kane Hemmings of Cowdenbeath picked up the Championship award while Rangers left-back Lee Wallace was voted the best player in League One with Peterhead's Rory McAllister winning the League Two award.
Pittodrie winger Jonny Hayes was awarded the goal of the season award following his stunning long-range drive against Celtic in February.