While Italy celebrated its seventh Tour winner, a jubilant France hailed its first double podium finish in 30 years as veteran Jean-Christophe Peraud and youngster Thibaut Pinot took second and third respectively.
"We are very happy today, it's a beautiful victory. Congratulations to the whole team," said Nibali's Astana team manager Alexandre Vinokourov.
Nibali beat Peraud by 7:37 and Pinot by 8:15 to become the sixth man to win all three grand tours after Belgian Eddy Merc kx, Frenchmen Jacques Anquetil and Bernard Hinault, Italian Felice Gimondi and Spaniard Alberto Contador. The Italian finished safely - as the sprinters contested the embers of the three-week Tour around the Champs Elysees - emulating the 1998 feat of Pantani.
Germany's Marcel Kittel produced a burst of speed to claim the final stage, his fourth stage win of the Tour and a repeat of his victory on the iconic Parisian landmark last year.
Nibali began the day with a near eight-minute lead and only needed to avoid a last-day crash to complete victory. Contador, who was hoping to add to his two Tour titles, crashed out in the 10th stage, riding 15 kilometres with a broken shinbone before pulling out, and last year's winner Chris Froome packed his bags after a crash on the cobbles on the fifth stage, the day Nibali opened a big gap over all his main rivals with a scintillating display on the treacherous lanes of northern France. "I was ready to take them on. And crashes are part of the race," Nibali replied when asked whether Froome and Contador's exits would undermine his title.
Nicknamed 'The Shark of Messina', Nibali stayed true to his aggressive self by attacking repeatedly on the big climbs, hammering the opposition in the mountains. While the 2012 Tour crowned a 'rouleur' in Wiggins and a climber the following year in Froome, this year's race belonged to a true all-rounder.
On Sunday, he just stayed safe in the bunch during the last stage as Kittel beat Norway's Alexander Kristoff and Lithuanian Ramunas Navardauskas.
The 137.5-km procession to Paris started from Evry in a festive atmosphere after the riders were transferred by plane from Bergerac, where all the distinctive jerseys were effectively sealed. True to tradition, Nibali and his team mates drank champagne while the peloton rode towards Paris at a snail's pace.
Nibali avoided trouble on the last stage, just as he did for the last incident-packed three weeks.
Pinot, 24, claimed the white jersey for the best under-25 rider, beating compatriot Romain Bardet, sixth overall, after cracking him in the Pyrenees. Peter Sagan sealed his third consecutive green jersey for the points classification - though he did not win a stage - while Poland's Rafal Majka was king of the mountains.
French outfit Ag2R-La Mondiale won the teams classification.