In what was a comfortable game for the Pittodrie club, who needed a draw to finish above their visitors, they were undone in injury time as Craig Reid prodded the ball into the net on one of the few occasions the Fir Park side showed any threat in the match.
However, the goal triggered a furious reaction from Aberdeen's players and officials, who claimed goalkeeper Jamie Langfield had been fouled by Motherwell's John Sutton in the build-up to the goal. Replays of the incident show the two colliding in the air while missing the ball, only for it to bounce off the bar and be turned in by Reid. Referee Steven McLean did not rule for any infringement.
McInnes, whose side had been second in the league since February, did not mince his words as the defeat meant they finish two points below Motherwell on 68, but also cost them a further two weeks off in the summer as well as an extra £240,000 for finishing in second place.
He said: "It was a couple of mistakes from the officials we feel leads to the goal. In the context of what happened it is a big thing, there is a considerable distance between where the foul was committed and where the free kick was taken. That's the first thing. Then there was the foul on Jamie Langfield. Sutton barges into him and doesn't get any connection on the ball and takes Jamie out, and they've scored on the back of it - a decision we feel cost us.
"While it's still 0-0 you're open to a bit of quality from them or a mistake. The mistake hasn't come from my players, we feel as though it has come from a decision, and that's why it's harder to take. I was delighted when I saw who we had to referee the game but I do think he's got it badly wrong.
"I need to say congratulations to Motherwell because over the course of the season they've done well. I don't want to sound as if this is sour grapes. We need to recognise their efforts."
Stuart McCall, the Motherwell manager, was philosophical in his analysis of the game's key moment.
"Whatever we got today, especially against Aberdeen we more than merited it," he said. "If you look at Sutton's goal which was a yard onside in the League Cup and was flagged offside, the goal Russell Anderson scores with the last minute of the game at Fir Park [in a 2-2 draw] when he forehand smashes it over, they say swings and roundabouts. It evens itself out."