Cavendish sealed his 25th stage win to move into a tie for third place on the Tour's all-time list, during an eventful day in which Froome gave up more than one minute to two-time former champion Alberto Contador.
To make things more worrisome for Froome, he once again had to fend for himself at the end because none of his withering Sky teammates could keep the pace. This is the second stage so far that they have been unable to support him, and with a tough mountain trek looming on Sunday rivals may try to take advantage.
Dutchman Bauke Mollema is 2 minutes, 28 seconds behind Froome, and Contador is 2:45 back — having both gained 1:09 on the leader.
"I'm just happy I've got an advantage of more than two minutes," Froome said.
Sky is down to seven riders — Edvald Boasson Hagen fractured his shoulder on Thursday and Vasili Kiryienka was disqualified earlier in the race for missing a time cut. Also, Brit Geraint Thomas is riding with a fractured pelvis.
"(Edvald's) a huge part of the team and we could really have done with him today and the same with Vasili," Froome said. "They're both really strong engines and the team is definitely weakened without those guys."
Contador, the Tour champion in 2007 and '09 who was stripped of his title the following year for doping, is now looking like a serious contender again after struggling in the Pyrenees. Froome knows that Sunday's massive climb up to Mont Ventoux could have a major bearing on the race.
"I think there will be more time won and lost on a stage like Ventoux than the last 20 (kilometres) on this stage," he said.
Contador's late attack Friday was timed to perfection and caught Froome cold.
"Near the end we saw that many riders were at their limit," Contador said. "There were a lot of people barely hanging on, and we couldn't have asked for a better result."
Cavendish, meanwhile, was preparing to "have some Champagne" after moving even with Frenchman Andre Leducq on the all-time list of stage winners.
"My team did an incredible job," Cavendish said. "They rode themselves into the ground."
His relief was clear to see as he rushed into the arms of teammate Sylvain Chavanel after the stage. On Thursday his teammates had put him into a great position to attack but he was beaten to the line by Marcel Kittel of Germany.
"Yesterday they gave everything and I let them down," Cavendish said. "The Tour de France is the most incredible race in the world. It means so much to me. When I think about it, it makes me want to cry."
Flat stages are normally relatively free of incident, but the 173-kilometre (107.5-mile) trek from Tours, which is surrounded by the Loire river, to Saint-Amand-Montrond in central France was quite the opposite.
With about a third of the stage gone, the main pack split into three and Alejandro Valverde dropped way out of contention after stopping to repair a puncture. None of the teams ahead waited and he lost a huge amount of time, dropping down from second overnight to 16th.
"That's a really unfortunate position for Valverde," Froome said.
Contador bounced back after being battered by Froome in the Pyrenees last weekend and losing more time in Wednesday's time trial.
"I only can say thanks, thanks and thanks to my whole team," the Spaniard tweeted. "Proud of all of you."
Victoria's Ryder Hesjedal remained the top Canadian in the overall classification in 54th place, 48:49 behind Froome. Quebec City's David Veilleux was 135th overall while Svein Tuft of Langley, B.C., was 180th.
The peloton had splintered after an attack from Cavendish's Omega Pharma QuickStep team, with Tony Martin leading the charge. Thankfully for Froome he did enough to stay with the small group forming at the front as it pulled away from the two groups behind.
The reason for Omega's attack was to try and shake off Kittel — who has won three sprint stages so far — and it worked to perfection.
"We just felt the wind wasn't in the right position," Cavendish said. "So we decided to ride harder, to make the peloton more tired and finally it broke."
Belkin showed no mercy, profiting from Valverde's mishap to push Mollema and countryman Laurens Ten Dam, who is now fifth, up the overall standings.
"I just hope that no team would do that to me if I had a mechanical problem," Froome said.
Belkin pushed so hard that Richie Porte, Froome's strongest teammate, had to drop back. If Froome is left all alone on Mont Ventoux, his lead could be further shredded.
Associated Press writer Jamey Keaten contributed to this report.