Before stunned onlookers, Farrar dropped his bicycle and stormed toward the Argos-Shimano team bus of rival sprinter Tom Veelers, shouting: "You don't do that to someone."
Argos Shimano riders pushed Farrar away from their bus while staff from the American's Garmin-Sharp team ran to pull him back to their own bus, which was parked nearby.
Neither Farrar nor Garmin-Sharp manager Jonathan Vaughters would comment on the rider's outburst.
Fabian Cancellara retained the overall leader's yellow jersey for a sixth straight day after the mostly flat 122-mile trek from Rouen to Saint-Quentin - almost tailor-made for sprinters except for a slight uphill near the end.
The barreling pack overtook three breakaway riders with barely 110 yards left, and Greipel wheeled out in front a split-second ahead of Matt Goss of Australia, who was second, and Juan Jose Haedo of Argentina, who took third.
Like in Greipel's sprint-finish victory a day before, a late crash tarnished the stage, and he counted himself "lucky" to avoid a spill two days in a row.
"Somehow I stayed on my bike," said Greipel, who turns 30 on July 16. "It was quite a tough finish there . . . and it was also luck on our part to catch the breakaway."
The top standings didn't change: Bradley Wiggins, the leader of Cavendish's Team Sky, was second overall, seven seconds behind the Swiss leader. Defending champion Cadel Evans of Australia was 17 seconds off the pace in seventh.
By holding the lead, Cancellara earned the right to wear the coveted yellow jersey for the 27th time in his career, a record for a rider who has never won the Tour.
The race got its first minor dose of rain Thursday, and another dropout: Germany's Marcel Kittel, who has endured gastric troubles for the last few days, pulled out to reduce the field to 194 riders.
Friday's sixth stage offers the last leg in the northern flats this week.