After Edward Ofere's goal four minutes into the second half, a David Raven own-goal and a close-range finish from Niall McGinn ensured all three points would be heading back to Aberdeen.
McInnes' team were second-best for large parts but he was pleased with the determination the Dons showed to overcome the one-goal deficit and pick up the three points.
The win secures Aberdeen's best finish in the top flight for 21 years, with them now 19 points clear of the Caley Jags in second place.
"The will to win was clear," said McInnes. "The conditions played a huge part in the game and in the first half we had to defend deeper. Inverness were excellent.
"The goalkeeper kept us in the game with two or three saves and it was perhaps harsh on Inverness.
"But at 1-1 the reaction was that only us would go on to win the game. We put pressure on them.
"From our experiences this season I could sense that we would go on and score, and so could the players. The crowd behind the goal got behind them and the goal was always to come."
Source: Yahoo/PA Sport