Thomas was just three seconds off yellow after Team Sky finished the team time trial second to BMC, whose Greg Van Avermaet took the race lead.
Defending champion Chris Froome is also out of contention for the overall victory but leapfrogged Slovenian Primož Roglič, the victor of yesterday's final mountain stage, into third on the general classification standings after he crossed the line today in second.
The Cardiff rider became the first Welshman to win the race when he crossed the finish line in Paris on Sunday.
Dutchman Tom Dumoulin finished second for Team Sunweb while Giro d'Italia victor Chris Froome (Britain/Team Sky) finished third.
The Team Sunweb rider's day did not get off to an ideal start when he could not find his time trial skinsuit in the morning.
"Nico [Portal, Team Sky sports director] told me to relax, take it easy and just make sure I won the Tour".
"It wasn't like I had to work for him as a domestique".
On the contrary, many Australians will feel happy for Thomas, who is well known to the domestic Australian cycling scene.
Froome struggled at times in the final kilometres of the final climbs on key stages, when Thomas was forced to counter threats by Dumoulin and Slovenian Primoz Roglic virtually on his own.
"I was a bit far back after the tunnel, but I was with Ferrari, and then Trek-Segafredo did a really good lead-out from behind and I managed to get John's wheel and I could start at a really good spot and I managed to pass John".
Afterwards, he embraced by his wife Sara and Team Sky principal Sir Dave Brailsford, and wiped away a tear.
Rangers trade Cole Hamels to Cubs
Hamels carried a 3.61 ERA at the end of June, before a rough July (1-3, 11.12 ERA) sent his ERA climbing and his price dropping. Chatwood walked six batters in the Cubs' 7-6 walk-off victory over Arizona on Thursday, giving him 85 walks in 94 innings.
"It's going to take a while to sink in", Thomas said before draping the flag of Wales over his shoulders during the podium ceremony.
"The strongest guy has won this Tour de France", Froome said.
His eventual victory had been a mere formality after Saturday's individual time trial stage which left him with a one minute 51 second advantage over second-placed Tom Dumoulin of the Netherlands.
The team's dominance in recent years and Froome's positive test for excessive levels of the asthma drug Salbutamol (before subsequently being cleared of any wrong-doing) fuelled the crowds' anger.
He is also the first Dutchman in 30 years to finish second at the Tour.
Dumoulin may or may not be back for another tilt at the yellow jersey next year. He rode in the 2013 Tour with a broken pelvis, saying it was "the worst pain I've ever experienced on a bike".
"We're a small nation and we really get behind anyone who's successful", Thomas said.
But Thomas, a key helper in Froome's previous four Tour wins, stepped up to the plate when required, countering risky attacks and threats from rivals, and sprinting to claim precious bonus seconds to show he was fully deserving of what was a historic win for Wales.
This victory will come in his ninth Tour, one fewer than the record for most appearances before winning, held by 1980 victor Joop Zoetemelk of the Netherlands.
Thomas finished third in the stage, 14 seconds behind.
"We spend a lot of time together, we train a lot together and I've seen how he's developed over the years".