"It was a sloppy goal to concede," Rowett said.
"We've given away a little bit too much space second half.
"But the team has shown incredible character."
And Kee, who came on when McGurk was knocked unconscious by his own keeper, was praised for his impact on the game, scoring again having started on the bench.
Rowett said: "I woudn't ever confess trying to tell a player he's better off being a sub.
"But it's great being able to bring on players of that quality.
"Games are very tight this season and you want to have someone who can change the game from the bench and Billy is always dangerous."
A lengthy stoppage, as Adam McGurk was stretchered off the pitch, meant it was a late break for both sides.
And Burton came out sharper, Rene Howe nearly putting them ahead, finding space in the box, only for keeper Scott Davies to tip the ball on to the woodwork.
At the other end Fleetwood's Gareth Evans rattled the post, having left two Burton defenders in his wake.
The game looked to be heading for a stalemate until a snap-shot from Jeff Hughes forced a corner.
From the set piece, Northern Ireland international Hughes surged through the crowded area and fired low past Lyness.
Town looked like they were going to hang on but at the death Phil Edwards flung in a long throw from the right and the ball bounced kindly for Kee to turn and fire past Davies.