With the rain pouring down for much of the day's racing between Maubourguet Pays du Val d'Adour and Bergerac, many riders suffered punctures and had to stop to make repairs.
Towards the conclusion of the stage, a large crash saw a number of riders go down, but Astana's Nibali was able to pick his way through the carnage and finish 24th, with Ramunas Navardauskas of Garmin-Sharp claiming victory.
With two stages left, Nibali's seven-minute advantage looks sure to see him claim the yellow jersey on Sunday, and he was pleased to have avoided the accident that could have seen his Tour hopes end in dramatic fashion.
"It was a hard day because of the weather and there was a moment of surprise with the crash but we got through it okay," the Italian said.
"We were close to the finish and so we'd moved back to let the sprinters take charge. We didn't want to take any risks.
"It [leading the Tour] is earning me a lot of attention and popularity, congratulations and prestige. For me personally, it pays me back for all the sacrifices that I, and all the people who have ever helped me, have made.
"I've travelled a long road since I was a boy in Sicily and made a lot of sacrifices and had lot of help from a lot of people in Messina and then in Tuscany, where I developed as a rider.
"I've been lucky to be able to do what I love the most and make my boyhood dream come true."