The Italian had set the pace on day one at Golfclub München Eichenried but entered the final round four shots off the lead before carding a closing 66 to set the clubhouse target at 15 under.
It looked like that may not be enough as Fitzpatrick entered the scoreable closing stretch in a share of the lead but the Englishman bogeyed the 17th before picking the shot back up on the last to set up the play-off.
Heavy rain began to fall as the play-off got under way and that may have helped Fitzpatrick as his second shot when they went back up the last plugged in the rough inches short of the water as he went for the green.
Pavan played the par five as a textbook lay up and a pair of pars sent to duo back to the tee.
Second time around Pavan played a poor second but his third was sublime to set up a birdie from two feet and, when Fitzpatrick failed to get up and down from the sand, Pavan was the champion.
Austrian Matthias Schwab had led by two with seven holes to play but he signed for a 71 to finish in a tie for third at 13 under alongside defending champion Matt Wallace, overnight leader Jordan Smith, Spanish duo Rafa Cabrera Bello and Alvaro Quiros, South African Christiaan Bezuidenhout and Italian Edoardo Molinari.
Cabrera Bello and Wallace had also held the lead at points on a thrilling final day in Munich but in the end it came down to a head to head battle.
A two time European Challenge Tour and Qualifying School graduate, Pavan won his first European Tour title at last season’s D+D Real Czech Masters and rediscovered that form this week, bookending the event with his two lowest rounds of the season.
“It’s amazing,” he said. “I thought I had a chance starting the day.
“I was playing very well coming into the week, I just hit a few bad drives – it’s always a little bit of an Achilles heel. This hole (the 18th) is not the best for me without the driver but I managed to make birdie.
“I was feeling the rush. I had a little pitching wedge and luckily I got a decent lie but it just felt great, it was really close.
“Two years ago at this moment I was really struggling. I can’t thank enough my coach, my caddie, my family, my wife – it’s really amazing.”
Pavan did not hold the lead on Sunday until he hit his final putt in regulation play – carding six birdies in a bogey free effort.
He birdied the first before putting his approach at the fifth to tap-in range and taking advantage of the par five sixth, with an 11 footer on the ninth putting him in a share of second.
A ten foot putt on the 16th after an excellent par save from the trees on the previous hole had him within one and when he got on the 18th green in two, he had set the target.
Fitzpatrick parred his first eight holes but got on the green at the par five ninth in two to join Pavan in second at the turn.
He was still one back when he birdied the 13th from eight feet but a brilliant second from the left rough and a putt from the fringe on the next had him in top spot.
A three putt par on the driveable 16th and bogey at the par three 17th after finding sand off the tee put the pressure on but Fitzpatrick hit a stunning three wood into the 18th green to set up a birdie.
“I’m obviously disappointed,” said Fitzpatrick. “It’s just been a tough season so far, really, not holing the putts. I’ve been playing well, that showed coming here and getting into a play-off. It’s a good week overall but disappointed not to top it off.”