A second gruelling mountain stage - the Tour's 14th - departing from Grenoble took in two category-one climbs as well as the Hors categorie slog up into Risoul.
Tinkoff-Saxo's Majka had been unable to hold Nibali off as the Italian secured victory in Friday's 13th stage, but a swift break with 10 kilometres to go secured victory for the Pole on this occasion.
Nibali did his best to hunt the 24-year-old down in the closing stages and came within 30 seconds after sensationally bursting clear of the peloton 5km from the line.
The Astana man's closest rival in the general classification, Alejandro Valverde, dropped a further minute off Nibali's pace, leaving the Italian four minutes and 37 seconds ahead and looking a dead cert for the title.
Owner of the white jersey, AG2R La Mondiale's Romain Bardet, benefitted from committed assistance from his team-mates to move within 13 seconds of Valverde, whose race for the Maillot Jaune looks run.
Meanwhile, Joaquim Rodriguez's quest to end the race as the King of the Mountains was boosted significantly as he claimed maximum points from both climbs to take sole ownership of the polka dot jersey.
The Katusha rider went into the stage wearing the jersey as Nibali had previously lead the climber's classification.
And the Spaniard's desire was evident from the beginning, the 35-year-old riding flat out to form part of an early 17-man breakaway.
Rodriguez's initiative was rewarded as he earned 10 points after being first up the Col du Lautaret, before repeating the feat on the Col d'Izoard to add another 25 points to his name.
But Rodriguez's heroics proved to be little more than a prelude to that of Majka as he wrote his name into the Tour's history books with a superb late charge.
Riders with tired legs will be relieved in Sunday's action as a much flatter run from Tallard to Nimes will favour the sprinters in the field.