Flood snatched all three points for the Dons three minutes from time when he drilled a superb 25-yard effort into the corner, but McInnes revealed that the Irishman had defied orders not to shoot from distance.
"It was a bit of quality that won the game, and a great strike from Willo," said the Dons boss.
"I'd said not to shoot from distance because Hibs usually have a lot of bodies centrally, but the space opened up in front of him and it was too inviting for him not to hit!
"I'm pleased Willo got another goal because I think he was great tonight, and he was in good company. I was delighted with the perseverance of the team. I felt the team on the pitch were the team to win the game.
"I always feel we have a goal in us, and the players believe that too. We've had a lot of late winners recently and they're always welcome. It's a good sign for any team."
See Flood's explosive goal below!