David Edwards scored early on and Sylvan Ebanks-Blake added a stunning second for Wolves, who ended a winless run that had stretched to 12 games, with Saunders being in charge of nine of those.
The result sees the Molineux outfit move out of the drop zone, and former Doncaster boss Saunders is now looking up rather than down.
"I was always confident we'd turn things round," said Saunders. "I know how to get a team to win - you've just got to keep believing what you're telling the players is right.
"Most of our performances have been good, but we've got the two goals to show for it here.
"When you've been on a losing run like we have you expect things to go wrong. I bet the players were thinking, even at 2-0, if Millwall score they'll get another one.
"We defended brilliantly, the back four were excellent and that's three games we've gone without conceding from open play.
"We pressed them throughout and stopped them building any momentum, we worked hard from the front to the back, and when they did pressure us we dealt with it well.
"They're a good team, it's not so long ago they were 10th, now we're right behind them."