There were few clear-cut chances which came as no surprise - before the game only leaders Celtic had conceded less than the 19 goals both sides had let in in the Scottish Premiership season.
But Aberdeen took it 1-0 thanks to Flood's late goal.
McInnes paid tribute to Flood's strike and said: "It was a bit of quality that won the game, and a great strike from Willo.
"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 gave his players an ear-bashing as he felt they fell short of the standards they have set for themselves during his short time at the club.
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."
Despite his frustration, Butcher could not resist a laugh at his own reputation, adding: "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!"