The Astana rider moved five minutes 26 seconds clear in the Maillot Jaune, with Alejandro Valverde his closest rival despite Tinkoff-Saxo's Majka winning his second stage of Le Tour.
But Nibali said he was always concerned by the 124.5-kilometre journey from Saint-Gaudens to Saint-Lary Pla d'Adet, with three category one climbs included in the relatively shorter stage.
"The four climbs in a row really hurt," Nibali said.
"The team did an amazing job. I'm a bit relieved. I feared this stage a little bit. With such an intense stage, you never know what can happen.
"It can explode in the first climb and then, what do you do? The plan, anyway, was to stay calm and stay altogether."
Polish climber Majka said his aim was to preserve the polka dot jersey, with four stages - including the individual time trial - to go.
"This is my first Tour de France and I already have two stage victories," Majka said.
"I really like the Tour de France now. Maybe, it's the best Grand Tour for me because the weather is good, unlike at the Giro.
"Our team had bad luck in stage 10 [with Alberto Contador crashing] but after that, Bjarne [Riis] and Oleg [Tinkov] said that we needed to fight for a stage victory.
"We didn't win one but three stages, and now with the polka dot jersey, I feel good.
"But there's still one hard stage to go, I will fight more because this jersey is really important for the team."