The final climb up Alpe d'Huez lived up to its billing with Quintana lighting it up after an almost perfect set up by his Movistar team-mates Alejandro Valverde and Winner Anacona.
As the climb started to bite Valverde attacked to provide Quintana an early bridging outpost while Anacona was already set further up the road as one of several riders in the break.
While Quintana was surging, Team Sky's Froome was relying on team-mates Richie Porte and Wout Poels to minimise the damage, as both riders earned every cent of their their respective salaries riding defensively.
Quintana piggy-backed off Valverde until he faded and did the same with Anacona to finish 1min 20 sec ahead of Froome and just 18 seconds behind stage winner Pinot (AG2R).
Froome heads into the final stage in Paris with a lead of 1min 12sec over Quintana. Valverde is third at 5min 25sec.
“We fought all that we could to try and gain the time we had lost on Froome, with an attacking strategy from far, far away from the finish, trying to isolate him at the Croix de Fer," said Quintana.
"Yet we couldn't open a big gap and we had to give all into the final ascent.
"Winner Anacona did an amazing job for me, riding strong and steady through most of Alpe d'Huez, and the whole team helped me much from the very start, but it wasn't to be today."
Quintana, the winner of the best young rider classification, was still very satisfied with his result and the work of his team, which fought to see the Colombian rise up on the leaderboard after he lost valuable time during the opening week.
"It's unreal," said Froome, after the final big test of the Tour. "I'm sure I haven't quite taken it all on board yet. It's an unbelievable feeling to be sitting here still wearing this jersey.
"There were so many things going through my mind going up that last climb. There were moments where I thought, 'Hold on a second I could be in danger here'. But then always having my team-mates with me and having Wout and Richie there all the way until the end.
"I thought of all the sacrifices and the weeks of training camps. Time away from my wife and my family. Everything starts going through your head and I was on my limit there.
"I was hurting going up that last climb. But I just had to find something else just to keep pushing and get through today.
"It was only 110km but it felt like it was 300. It was such a hard stage."
For Pinot it was a redemptive ride after a less than stellar Tour. His gritty win was the third for the French in 2015 and came after he too had bridged to a team-mate, Alexandre Geniez, who was named as the most aggressive rider on the stage.
Pinot then faced off against a determined Ryder Hesjedal (Cannondale-Garmin) and finally dropped the Canadian before resisting the charge of Quintana in the final two kilometres.
Pinot, Quintana and Hesjedal topped the stage podium with just 41 seconds between first and third after 110.1km of racing from Modane Valfréjus to Alpe d'Huez.
The stage started slowly but ramped up quickly on the Hors Category Col de la Croix de Fer.
Geniez attacked from the gun taking Ramunas Navardauskas (Cannondale-Garmin) with him before adding Lars Bak (Lotto-Soudal) and Nicolas Edet (Cofidis).
The four riders built a maximum lead of four minutes before Geniez took the race into his own hands before the summit of the Col la Croix-de-Fer.
While Geniez was going solo Movistar launched a well planned move with 3km to go to the top of the climb.
Valverde was first to attack Froome then Quintana a kilometre further along before joining up before the top of the Col de la Croix de Fer. The move left the yellow jersey isolated, but he didn't panic and there was a regrouping on the descent.
With Geniez in the lead, Pinot, Anacona, Hesjedal and six other riders counter attacked with 50km to go.
Geniez hit the foot of Alpe d'Huez with an advantage of two minutes while Froome and Quintana were at four minutes.
Now solo, Pinot caught Geniez with 9km to go as Hesjedal did the same. Behind Valverde and Quintana repeatedly attacked Froome 11km from the finish.
After Valverde had exhausted himself Quintana latched on to Anacona who assisted for another two kilometres.
Pinot made his winning move for the stage victory with 6km to go and resisted Quintana who crossed the line in second position.