VERSAILLES, France, July 8, 2012 (AFP) - He closed with a 67 for an eight-under-par total of 276 and a one-stroke victory over Italy's Francesco Molinari who carded a day's best 64.
It was 31-year-old Siem's first Tour win since the Dunhill Championship in South Africa eight years ago.
Home hope Raphael Jacquelin was alone in third a further stroke back after signing for a 69.
Molinari started the day eight behind joint leaders David Howell and Anders Hansen but he quickly overtook them and finished with a 12-foot putt at the last for a remarkable nine birdies in 16 holes, an inward half of 29 and a best of the week 64.
The Italian Ryder Cup player than sat back and waited to see if anyone cvould match him with the leaders two hours away from the end of their day.
For a while it looked like he might stay atop the leaderboard only for Siem to sneak closer and then go in front by splashing out of sand to seven feet at the long 14th.
But he still had the tough closing four holes at the Albatross course to negotiate where water is an omni-present threat.
A birdie at 15 put him two ahead and that proved to be crucial as he bogeyed the treacherous par-four last.
Siem is the third German to win the French Open after Bernhard Langer in 1984 and Martin Kaymer in 2009.
Excited though he was, Siem declined to follow the example of last year's winner, Thomas Levet of France, who promptly jumped into a greenside lake and broke a leg.
"I'm just going to have some nice French champagne," the German said. "I've had so many tournaments I kind of destroyed this year and I am so happy I got it done.
"It's all about winning in the end and now I'm in The Open, which is unbelievable."
Justin Rose came joint ninth and Graeme McDowell was in a tie for 17th, while world No.3 Lee Westwood climbed 18 places to 40th with a closing 70.
That came a day after it looked as if he might be pulling out with knee and groin trouble after he slipped walking to the first tee.
"The leg is fine - it wasn't a problem today," Westwood said, after completing his final round before The Open at Royal Lytham starting on Thursday week.
Leading final scores on Sunday in the French Open at the par-71, Le Golf National course:
276 - Marcel Siem (GER) 68-68-73-67
277 - Francesco Molinari (ITA) 71-68-74-64
278 - Raphael Jacquelin (FRA) 68-71-70-69
279 - David Lynn (ENG) 67-72-72-68, Ian Poulter (ENG) 72-69-69-69, David Howell (ENG) 70-70-67-72
280 - Brendan Steele (USA) 70-70-71-69, Henrik Stenson (SWE) 68-73-69-70
281 - Soren Kjeldsen (DEN) 70-71-71-69, Justin Rose (ENG) 71-73-68-69
282 - Michael Campbell (NZL) 71-74-70-67, David Drysdale (SCO) 70-70-72-70, Nicolas Colsaerts (BEL) 70-72-69-71, Anders Hansen (DEN) 70-68-69-75
283 - Alexander Noren (SWE) 70-67-74-72, Thongchai Jaidee (THA) 66-75-70-72