Although the mishap is not expected to impact Armstrong's bid to win the world's most famous cycling race, it was the first hint of trouble he has suffered during this year's competition.
Armstrong fell late in the 173-kilometer ride from Bagnoles-de-l'Orne to Avranches, a town rich in history that sits close to the 11th Century abby of Mont St. Michel.
Another of the tour's leading riders, France's Laurent Jalabert, went down in the brief pileup that claimed Armstrong.
Although the riders involved were up quickly and worked hard to try to regain contact with the peleton, they were judged to have been too far behind the pack at the finish to be given the same time as the race winner. Both Armstrong and Jalabert wound up 27 seconds behind McGee.
Igor Gonzalez Galdeano of Spain, who has headed the overall standings for most of the tour, remained in front. He had a four-second lead over countryman Joseba Beloki and a 12-second advantage over Jorg Jaksche of Germany.
Armstrong began the day in third place, seven seconds behind. But the fall dropped him to eighth place, 34 seconds back. Going into the mountain stages last year, Armstrong was more than eight minutes behind, so he is expected to be able to overcome his current deficit.
Gonzalez Galdeano, however, is a formidable opponent who finished fifth in last year's tour.
A three-man breakaway opened a lead that grew to five minutes, 20 seconds Saturday, but the peleton eventually caught the group to set up a sprint to the finish.
Pedro Horillo of Spain appeared to have the victory in hand, but he threw up his arms in celebration a moment too soon and saw McGee storm past him at the line. McGee, 26, is the second Australian to win a tour stage this year. Robbie McEwen won a stage earlier in the event.
Jaan Kirsipuu of Estonia actually edged Horillo as well for second place Saturday while the rest of the top five were taken up by Horillo, McEwen and Erik Zabel of Germany.
Sunday's stage will be another relatively flat ride of 217 kilometers to Plouay, after which the riders will face an individual time trial on Monday. Armstrong is expected to dominate the two individual time trials in the race and could actually regain the overall lead Monday.
The first major mountain stage comes next Thursday in the Pyrenees.