Dupont crossed before the interval thanks to superb play from Virimi Vakatawa on both occasions as Les Bleus prepared for next weekend's potential title decider with Ireland, which will also be played behind closed doors at Stade de France because of the coronavirus pandemic.
Wayne Pivac's visitors lost a fourth straight international for the first time since the summer of 2016. They will host Scotland in the Six Nations, which had been put on hold since March because of the COVID-19 outbreak, in seven days' time.
The match had been at risk of not being played at all because of player release issues between the French federation and the Top 14 league with Fabien Galthie's side only meeting up six days before the match.
"We won the match with one training session in the week and we scored five tries against the Welsh. It's not nothing," Galthie said.
"Before saying there are things we can improve on I'm very happy to have managed to start like this after such a long time away," he added.
Galthie made three changes from loss to Scotland in March as Teddy Thomas, Vincent Rattez and Cyril Baille replaced the injured Damian Penaud, centre Arthur Vincent and the retired Jefferson Poirot.
Pivac's captain Alun Wyn Jones equalled former New Zealand skipper Richie McCaw's record of 148 Test appearances as hooker Sam Parry and winger Louis Rees-Zammit were handed international debuts from the bench.
Pivac's men opened the scoring in quick fashion as Leigh Halfpenny crossed for his 15th Test try on 60 seconds after Gregory Alldritt dropping Dan Biggar's kick-off.
Biggar kicked his first penalty goal five minutes later before France prop Baille opened his international account just before the quarter of an hour mark.
As the home side made ground into Wales's half after 20 minutes, back-rower Francois Cros carried well and Bernard Le Roux cleared Jones out at a ruck.
As the pair fell to ground the Racing 92 lock's right elbow made contact with the second row's face but referee Karl Dickson missed the incident and it was not picked up by the television match official.
Biggar kicked another penalty before the hosts took the lead after Vakatawa's first display of class after half an hour.
The New Zealand-born centre found space near the touchline before off-loading with one hand to find winger Teddy Thomas.
Dupont's support line was impeccable and picked off Thomas' pass to cross for his opening try and Romain Ntamack's conversion made it 14-13.
The lead was extended five minutes before the break as Vakatawa again found space behind the defensive line before drawing Halfpenny to send Dupont over for his maiden international double.
Ntamack and Biggar traded shots at goal and Galthie's men had a 24-16 advantage with a quarter of the match to play before Biggar failed with an effort.
Winger Louis Rees-Zammit made his Test bow with 17 minutes to go before Biggar missed the chance to cut the gap to five points once again as his long-range penalty drifted to the left of the posts.
The victory was sealed with a quarter of an hour left as the hosts captain Charles Ollivon charged over and a Ntamack conversion made it 31-16.
Replacement prop Nicky Smith crossed from short range but Biggar missed the extras leaving eight points in total on the tee before Teddy Thomas crossed for les Bleus fifth try with five minutes to play.