Commons' shot was deflected into the Saints goal by Liam Craig in the Scottish Communities League Cup tie.
And the stadium announcer declared Craig had scored an own goal in a match Neil Lennon's team ended up winning 5-0.
However, Scotland midfielder Commons still bagged the match ball at the end of a one-sided 90 minutes.
He grinned: "I don't think the first shot was going in. It was more of a cross than a shot. But I am taking the hat-trick.
"I have the match ball. It was a good move that led to the first goal. If their defender hadn't put it in one of our players probably would have.
"I listened out for the tannoy announcement and they didn't say my name so I thought: 'Oh, I'll give it to somebody else'.
"When I was taking the penalty in the second half I certainly didn't think it was for the hat-trick. I thought it was for the second goal. But I will definitely take it.
"I tried to get my shots away and work the goalkeeper. I scored against St Johnstone earlier this season and knew I was capable of it."
Commons was delighted Celtic managed to bounce back from their shock 2-0 defeat to Kilmarnock in the SPL at Parkhead on Saturday.
He added: "We worked hard, played with a good tempo and got the rewards. We scored good goals and kept a clean sheet.
"We also had fresh legs in Victor Wanyama and Scott Brown. They brought a lot of energy back into our play in midfield.
"Then we had Gary Hooper playing up front as well. He gives you that movement and goal threat up front.
"Everything that was missing on Saturday we put into practice against St Johnstone. It was good to get the win and put the defeat behind us."