The Team Sky rider secured his first Tour by almost two minutes ahead of Tom Dumoulin (Sunweb) with defending champion and team-mate Chris Froome, third.
The stage was won by Alexander Kristoff (UAE Team Emirates) ahead of John Degenkolb (Trek-Segafredo) and Arnaud Démare (Groupama-FDJ).
Thomas, known as "G," was a support rider during Froome's title rides but he became Sky's undisputed leader when Froome cracked in the gruelling 17th stage through the Pyrenees.
He claimed the yellow jersey by winning Stage 11 in the Alps, followed that up with another victory atop Alpe d'Huez a day later, and defended his advantage through the Pyrenees.
The best placed Australian was EF Education First Drapac's road captain Simon Clarke who finished 100th overall at three hours and 15 minutes behind Thomas.
"It's unbelievable," said Thomas. "It's going to take a while to sink in. Normally, this stage is really hard but today I just seemed to float around it - I had goosebumps going around there.
"To ride around wearing this (the yellow jersey) - it's a dream. With the boys - that's the main thing for the whole three weeks, we stuck together through some tough times, stayed strong."
The final stage featured the traditional procession into Paris and on to the Champs-Elysées where the race action started.
Soon to be retired Sylvain Chavanel (Direct Energie) was given the honour of leading the peloton on to the pave to celebrate his 18th Tour participation before a pedal was turned in anger.
Silvan Dillier (AG2R), Taylor Phinney (EF Education First-Drapac)), Michael Schär (BMC), Damien Gaudin (Direct Energie), Nils Politt (Katusha-Alpecin) and Guillaume van Keirsbulck (Wanty-Groupe Gobert) set out on a powerful break but which never extended its lead on the peloton by more than 40 seconds. The catch came right on the bell lap with seven kilometres to go as Politt resisted for another two.
The remaining kilometres were spent jockeying for position before the mass finish free for all. Démare made the first move but Kristoff had too much power on a course tailor-made for his talents.
"It's a dream come true," Kristoff said after the stage. "I've dreamt about this victory for many years. I've been close many times but never managed to beat the faster guys like Cavendish, Greipel or Kittel. But today they're not here - they're out after the mountains - and today I was the fastest so I'm super happy."