But Flynn conceded his heart was in his mouth when Brentford were awarded a 95th-minute penalty that could have denied his side a return to the npower Championship at the first attempt.
Brentford had their chance to seal automatic promotion themselves in the dying seconds after Clayton Donaldson had been bundled over in the box.
But on-loan Fulham striker Marcello Trotta wrestled the ball from first-choice taker Kevin O'Connor and blasted his penalty against the crossbar.
Rovers broke straight away and James Coppinger's injury-time winner settled the promotion shoot-out in a game almost totally dominated by the home side.
"We showed in 90-plus minutes exactly why we are worthy champions. We soaked up everything Brentford had and then hit them on he break," Flynn said.
"We stuck to the game-plan and had a few decent chances in the first half, were very solid and strong and played with our heads as well as putting our bodies on the line. That's experience."
Flynn, who said he wanted the manager's job full time when his contract expires on Sunday, added: "When they got the penalty, and I wasn't sure what it was for, a lot goes through your mind, but that is all history now.
"We've worked very hard for this and have stuck together and this is what you get if you keep doing what you are good as as we did."