CANTERBURY, England—The Predictor-Lotto rider, who already has three green jerseys to his name, outsprinted Norway's Thor Hushovd and Belgian Tom Boonen for his 12th Tour stage victory.
McEwen crashed 21 km from the finish line but was soon back on his bike with a bruised knee and a sore wrist.
The 35-year-old Australian entered the last straight safe in the bunch and claimed an impressive win with a late burst of speed.
"I can't believe I've won, the moment I crashed I thought that's that, and even my Tour could have been over," McEwen told reporters.
"But I pushed through and I've really got to thank my team mates for the work they did to bring me through."
Yellow Jersey
Swiss Fabian Cancellara of the CSC team retained the overall leader's yellow jersey after finishing comfortably in the peloton.
Briton David Millar, who finished 13th in Saturday's prologue round the streets of London, took the polka dot jersey for the best climber after a 165-km breakaway and is third overall.
"I just want to say thank you to the British public for the support they've given us," said Millar.
"I just rode out of my skin today and that was a thank you to everybody for coming out, that was amazing."
The stage started from Greenwich and went through the county of Kent in south east England, watched by an estimated two million people.
Millar broke away some seven km after the start and was soon joined by Frenchmen Stephane Auge and Freddy Bichot, Ukraine's Andriy Grivko and Belarus's Aleksandr Kuschynski.
The escapees built a six-minute gap with Millar and Grivko being dropped 35 km from the finish line. Cofidis rider Auge then went solo only to be swallowed by the peloton with 18 km remaining.
British hope Mark Cavendish lost any hope of clinching victory after mechanical problems forced him to change bike twice in the last 20 km.
Spaniard Eduardo Gonzalo Ramirez of the Agritubel team was the first casualty of the Tour. He was forced to retire with a shoulder injury after smashing the windscreen of a Caisse d'Epargne car.
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