Kee struck in the 27th minute with a fine turn and shot before Wycombe were reduced to 10 men after the break when Charles Dunne picked up a second yellow card on 48 minutes.
Kee duly punished the Chairboys with his second, scoring from the spot four minutes later to seemingly kill the game off.
Matt McClure pulled one back for Wycombe in stoppage time but Rowett's team were worthy of the win and the manager hopes his side will now get even better.
"On the whole it was probably our most controlled performance of the season in terms of a defensive and attacking threat," he said.
"You can see what a difference the likes of Billy make, that's three goals in two games and Adam McGurk too - they worked really, really well as a partnership and it was really pleasing.
"Overall the balance was a bit better, more focused with an emphasis on teamwork and getting that team ethic back that we need to have. We made it a little nervy the last minute or two which I've said to them we have to do a bit better and play with more control.
"When we've played against 10 men we've occasionally struggled, such as early on this season against Rochdale.
"We did that better at times and took more care of the ball and up until they scored you could see the frustration settling in on their side - it looked like the game would be dead and buried."