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."
Hibs counterpart Terry Butcher conceded that Flood's strike deserved to win the game, but he laid into his players for delivering their worst performance since he took over as manager.
He said "It was a wonderful strike, but I'm disappointed with the way we played. We've come nowhere near the standards we've set before.
"It's the worst that we've played since Maurice (Malpas) and I came here. It's the first time I've had a go at them.
"There were a few eyes and scary faces, a few things slammed about. I don't accept a drop in performance like that - I think they know now that they shouldn't do it again!"