Lee's magnificent solo effort completed the turnaround for Bolton after imposing Serbia international Nikola Zigic headed City into an early lead.
His strike was cancelled out by Marcus Alonso's header before Wanderers won a penalty in the second half after Birmingham captain Steven Caldwell was ruled to have handled in the box.
Keith Andrews coolly slotted home the spot-kick before they closed out the match through Lee's effort that had Freedman raving.
"It was a wonderful goal from a wonderful player and he deserves all the credit he gets because he had a horrible injury and he's worked so hard to get back from it," he said.
The win comes after Bolton suffered back-to-back defeats to Peterborough and Sheffield Wednesday and Freedman was delighted that his team got back on track.
He added: "We put everything together and to do it in front of the home fans is all the more pleasing.
"We targeted the midfield as an area where we could dominate the game and we certainly did that throughout.
"We moved the ball around well and to get the win was great for everyone."