The Italian went solo on the lower slopes of the Pyrenean climb to win by over a minute from Thibaut Pinot (FDJ.fr). The Frenchman in turn moved up to second overall while compatriot Jean-Christophe Peraud (Ag2r) rose to third, both at the expense at Alejandro Valverde (Movistar) who slipped to fourth overall.
Nibali now leads the race by a hefty seven minutes and ten seconds with Saturday's time trial the only stage remaining that's expected to have any bearing on overall positions.
But with Pinot, Peraud and Valverde all within 15 seconds of each other, the minor places are far from settled.
Rafal Majka (Tinkoff-Saxo) meanwhile finished today's stage in third place to secure victory in the King of the Mountains competition. Yesterday's stage winner had set off in lone pursuit of Nibali but was caught by the three man chase group of Pinot, Peraud and Teejay van Garderen (BMC).
Peraud's team mate Romain Bardet also gained a few token seconds on Valverde, attacking the third group on the road in the closing kilometre. He remains in fifth place overall.
After yeterday's 124.5km affair, today's was another short blast of a stage, totalling 145.5km that spiralled from Pau, over the Col du Tourmalet to the ski resort at Hautacam, near Lourdes.
A 20 rider group formed the early breakaway. It comprised Mikel Nieve (Sky), Jesus Herrada, Jon Izaguirre (both Movistar), Yuriy Trofimov (Katusha), Alessandro De Marchi, Marco Marcato (both Cannondale), Lars Boom (Belkin), Jan Bakelants (Omega Pharma-QuickStep), Blel Kadri (AG2R), Matthieu Ladagnous (FDJ), Daniel Oss (BMC), Bryan Coquard, Kévin Reza, Thomas Voeckler (all Europcar), Julien Simon (Cofidis), Sylvain Chavanel, Marcel Wyss (IAM), Bartosz Huzarski, Tiago Machado (NetApp) and Florian Guillou (Bretagne-Seche Environment).
After blowing apart on the 2,115m high Tourmalet, tackled from the east side through La Mongie, Nieve and stage eight winner Kadri summited at the front.
Basque Nieve subsequently dropped the Frenchman at the foot of Hautacam. But carrying just a minute's lead on a main group spearheaded by Astana, his time out front was limited.
It was Lampre-Merida's Chris Horner who proddded Nibali into life, attacking with over 10km of the 13.6km climb remaining.
With the rest of the group more concerned with how they fare against each other, the pair were left to it. Then when Nibali decided Horner's speculative move wasn't quick enough with over 9km to go, he lowered himself onto the drops, issued a single acceleration and rode away. Less than a kilometre later he powered straight past Nieve.
The only resistance Nibali's attack faced was the climb's varying gradient and the protruding elbow of a fan who appeared to be on her mobile while looking the wrong way up the road.
Pinot's attacked created a little more response with Van Garderen and Peraud quickly following him. Valverde, meanwhile, was briefly dispatched out the back of what remained of the disintegrated group.
Pinot and Van Garderen did the most part of the driving of this group - which was less a chase of Nibali than an attack on Valverde. Peraud meanwhile clung on. Once recaptured, Majka also took on a passneger role, safe in the knowledge he just needed to finish within the top six to stop yellow clad Nibali claiming his spots.
It was he who opened the final skirmish for the line, but was superseded by a strong looking Pinot. Historically a dreadful time triallist, Pinot's small gains on his other podium rivals today will unlikely be enough to keep him in the top three come the end of the Tour.
Haimar Zubeldia was the other rider to make noticeable gains on GC. Finishing in ninth on the stage, he knocked Pierre Rolland (Europcar) out of tenth overall.
Tour de France 2014, stage 18: Pau to Hautacam, 145.5km
1. Vincenzo Nibali (Ita) Astana in 4h 4m 17s
2. Thibaut Pinot (Fra) FDJ at 1:10
3. Rafal Majka (Pol) Tinkoff-Saxo at 1:12
4. Jean-Christophe Peraud (Fra) Ag2r at 1:15
5. Tejay van Garderen (USA) BMC Racing Team at same time
6. Romain Bardet (Fra) Ag2r at 1:53
7. Bauke Mollema (Ned) Belkin at 1:57
8. Leopold Konig (Cze) NetApp-Endura at same time
9. Haimar Zubeldia (Spa) Trek at 1:59
10. Alejandro Valverde (Spa) Movistar at same time
57. Geraint Thomas (GBr) Sky at 19:01
Overall classification after stage 18
1. Vincenzo Nibali (Ita) Astana 80h 45m 45s
2. Thibaut Pinot (Fra) FDJ at 7:10
3. Jean-Christophe Peraud (Fra) Ag2r at 7:23
4. Alejandro Valverde (Spa) Movistar at 7:25
5. Romain Bardet (Fra) Ag2r at 9:27
6. Tejay van Garderen (USA) BMC Racing Team at 11:34
7. Bauke Mollema (Ned) Belkin at 13:56
8. Laurens Ten Dam (Ned) Belkin at 14:15
9. Leopold Konig (Cze) NetApp-Endura at 14:37
9. Haimar Zubeldia (Spa) Trek at 1:59 at 16:25
23. Geraint Thomas (GBr) Sky at 56:26
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