Pavan birdied the second extra hole after both players had finished tied on 15 under par, two shots ahead of a seven-strong group including overnight leader Jordan Smith and defending champion Matt Wallace.
Fitzpatrick enjoyed a massive stroke of luck on the first play-off hole when his approach from 285 yards somehow plugged on a downslope just inches from a water hazard, but a poor pitch meant he could only match Pavan’s par.
The players returned to the par-five 18th and, after Pavan hit a superb third shot from the rough to tap-in range, Fitzpatrick mishit his bunker shot and could not hole a lengthy birdie attempt.
Pavan had set the clubhouse target after a flawless closing 66 and looked on as Fitzpatrick had an eagle putt to win on the 72nd hole, only to leave it short.
Wallace also needed to birdie the last to match Pavan’s total but found the water twice and did well to salvage a bogey six.
“It’s amazing to be honest,” Pavan said.
“I thought I had a chance starting the day. I was playing very well coming into the week and just hit a few bad drives, it’s always a little bit my Achilles heel.
“This hole (18th) is not the best for me without driver but I managed to make birdie and it’s been amazing.
“I was in a play-off in qualifying for the US Open with five guys for one spot and I three-putted the first and then you go home with nothing.
“Here at least the worst you finish is second but it’s very satisfying to get the win, it’s so hard, so difficult.”
Fitzpatrick admitted he is enduring a difficult season and was frustrated not to get over the line in Munich.
“It’s disappointing. (I have) been playing well. Obviously that showed coming here, and getting into a playoff, which has been great,” Fitzpatrick.
“It’s a good week overall, but yeah, disappointed not to top it off.
“Had a bit of a look the first playoff hole, but yeah, it’s just been a tough season so far, really. Not holing the putts. Missed a chance on 16 there – didn’t hole it.”