Bowyer received a yellow card from referee Lee Mason after a late lunge at Gibson who was starting his first Barclays Premier League game since April.
The United chief fumed: "The Bowyer tackle in the first half, I thought it was a red card. He's gone over the top of the ball."
He added: "Bowyer has been given a yellow card so nothing can be done about it (retrospectively).
"But it's a dangerous tackle."
Ferguson's anger was also not helped when replays suggested Blues striker Nikola Zigic had been guilty of handball and committing a foul in the build-up to Bowyer's point-saving goal.
But in the cold light of day he can reflect with satisfaction on United heading into the New Year on top of the table.
They have lost only two league matches during 2010 and remain unbeaten in the top flight during the current campaign.
Ferguson said: "I always say if we get to that top position on New Year's Day, then we've always got a great chance.
"There's five or six teams who are all contesting that area towards the top of the league."
Source: PA
Source: PA