With the score at 0-0, the Bees were awarded a 95th-minute penalty that would have denied Rovers automatic promotion but the hosts contrived to miss the spot-kick before Rovers raced up the other end to score on the break.
And with Bournemouth only drawing at Tranmere, Flynn's men went from the prospect of having to face a play-off campaign to champions in the blink of an eye.
After claiming such a remarkable triumph, Flynn could have been forgiven for celebrating in style but the Welshman insists he had no trouble getting back to work this morning.
He told BBC Radio Five Live's Sportsweek programme: "I enjoyed my night last night, obviously, but back to work this morning that's for certain."
While the manager may have had a reserved celebration, his players are sure to have made the most of their moment, and Flynn was delighted for his troops after many of them were part of the side that was relegated from the Championship last season.
"The lads have earned it and deserved it for the season they've had and what they've put in," he went on.
"Last year was a disaster, any relegation is a disaster but in many ways it was a difficult period for the club but to bounce back so quickly and do so well, it was even more enjoyable."
He added: "It was a difficult season for them last year. They tried a few things and it didn't come off.
"The fans were superb in terms of the support they have given the club when things aren't going well and things weren't going well last year and to give them something back like this, it means so much.
"The squad are so proud to play for the club which means a lot to them and a lot to the fans."
James Coppinger was the man who grabbed the vital goal after breaking forward with team-mate Billy Paynter and Flynn joked that divine intervention may have played a part in the late winner.
"Right in front of me in the dugout hunched on his knees was Billy Paynter who's come over, and I said him 'what are you doing here?' and he said 'I'm praying'.
"And the clearance actually went straight to his foot and he was through on goal and we were two-on-one with the goalkeeper.
"It was an amazing scene to be fair."