The British rider stayed rooted to his saddle as he left Alberto Contador for dead with an attack which, if not easy on the eye due to his jutting elbows and nodding head, proved ruthlessly efficient.
He crossed the line 29 seconds ahead of Colombian Nairo Quintana, who had launched an attack 13km from the finish.
Team Sky's Froome, who showed he is unbeatable on a single climb, now leads Dutchman Bauke Mollema by 4:14 in the overall standings.
This is roughly the same as Alberto Contador's winning margin over Andy Schleck when the Spaniard won the Tour in 2009 after three weeks of racing.
Contador, the 2007 and 2009 champion, crossed the line in sixth place after the 242.5-km 15th stage, 1:40 behind Froome to leave him third overall, 4:25 off the pace.
Mollema was eighth on the day, six seconds behind Contador, who was clearly stunned.
"He is very superior to everyone in the mountains," Contador told reporters."
"He showed it in the Pyrenees and once again here. I did what I could, climbing at my rhythm but he was too strong.
"I came here to win but Froome is very strong and every time he takes time from me."
His sports director Philippe Mauduit said: "We will talk and see what tactics we can set up for the rest of the race."
Froome had lost 1:09 to Contador on Friday's flat stage after being trapped by the Spaniard's Team Saxo-Tinkoff, but he came back with a bang.
"I did not imagine this. This climb is so historic, it means so much to this race. I did not see myself winning. I thought I had to surrender the stage to Quintana," Froome, who spent most of the ascent talking to the team car on his radio, told reporters.
Froome is the first yellow jersey wearer since Eddy Merckx in 1970 to win on top of Mont Ventoux, a climb packed with history and the scene of British rider Tom Simpson's death in 1967.
"My goal was to take time from my GC (general classification) rivals," added Froome, who had to be supplied with oxygen at the finish after the 20.8-km climb at an average gradient of 7.5 per cent.
"I thought Quintana would win but in the last two kilometres he could not follow."
Quintana, who took the young rider's white jersey from Pole Michal Kwiatkowski, said: "I had already made an enormous effort and when he caught me I had not much left in the tank."
ISOLATE FROOME
A 10-man breakaway formed early and tried to build a decent lead, but when Pierre Rolland slipped back into the peloton, his Europcar team upped the pace.
France's Julien El Fares was dropped and the other escapees were kept within range with Quintana's Movistar team setting the tempo around 100 kilometres from the finish.
The barren summit of Mont Ventoux was draped in a thin veil of cloud as Team Sky hit the front and upped the pace six kilometres from the base to put Froome in a perfect position at the foot of the climb.
On Bastille Day, Frenchman Sylvain Chavanel powered away from the lead group, but he was quickly swallowed up by the Sky-led main bunch.
Peter Sagan, also part of the breakaway, rode on his back wheel and showboated to the cameras after claiming 20 points to stay in charge of the green jersey, before he too was caught.
The fun and games were cut short as Team Sky's Peter Kennaugh took his turn at the front of the peloton.
Australian team mate Richie Porte then took over and his long drag up the shadowy part of the mountain thinned the peloton until only him, Froome and Contador remained.
The Spaniard had no answer to Froome's attack seven kilometres from the finish, just like he could not respond to his rival's acceleration in the previous mountain-top finish in the Pyrenees.
There are, however, two gruelling stages left in the Alps, with several tough climbs on the menu.
These will provide the perfect terrain for Sky's rivals to try to isolate Froome, like they did in the second Pyrenean stage.
Some of the top names in the sport were humbled on Sunday.
Andy Schleck, the 2010 champion who had targeted the stage win, almost rode into a low dry stone wall in the first part of the climb and finished 10:42 behind.
Australian Cadel Evans, who won the race two years ago, crossed the line 8:46 off the pace.
"It was a terrible day for me," he said.
"I came to the Tour de France with high expectations but I did not live up to them."
