After a six-hour wait to tee off in a third round that never materialized, Pettersson beat David Gilford with a par at the first hole of a sudden-death playoff for his first European Tour victory.
Both Pettersson, a Swede based in the Raleigh, N.C., and Gilford, from England, finished at 2-under 142 for the two rounds.
'It's a shame it had to come after only 36 holes but at least I had to come through a playoff to win,' the 24-year-old Pettersson said.
Gilford hit his approach shot on the playoff hole, the 18th, through the green and into the rough soaked by thunderstorms, then took three to get up and down for bogey. Pettersson hit a 6-iron to 20 feet and two-putted for par to win a spot on the European PGA Tour through 2004.
Pettersson was the seventh first-time winner on the European Tour this year.
'I'm usually a pretty calm guy but I was shaking a bit on the green out there, ' he said. 'I came close to winning last year. And I've had three top-fives this year. A victory was my goal this year. I knew deep down I could do it. But it feels good to get it so quickly.'
Pettersson, who flew to Portugal from the United States last Monday and plays the European Tour as a transatlantic commuter, won $108,500 to move to fifth on the European money list. Winnings were reduced to 75 percent of the scheduled purse.
He will fly home to the States on Monday but will be back for the Spanish Open in two weeks.
'Ultimately I want to play the U.S. tour, to play against the world's best, ' Pettersson said. 'But equally I would love, like any European, to win a Ryder Cup place. I haven't finalized my future plans yet.'
The last time a playoff was used to break a 36-hole deadlock was at the Welsh Open last August, when Ireland's Paul McGinley beat England's Darren Lee and Scotland's Paul Lawrie.
Full-field scores from the Algarve Open de Portugal