Payet, who missed France's World Cup triumph through injury, opened the scoring on the stroke of half-time and added his second just after the hour mark at the Stade Velodrome.
Valere Germain slotted home the third in the 89th minute before Florent Thauvin added the fourth in injury time to secure a comfortable three points on a night which saw the World Cup trophy shown off to the crowd who also warmly welcomed back their world champion players Adil Rami and Steeve Mandanda.
The VAR (Video Assistant Referee) system had debuted at the World Cup in Russia and it made its entrance in the French top flight on Friday just before the half-time whistle.
Referee Ruddy Buquet had originally signalled for a corner after a header from Germain had come off the arms of Toulouse defender Kelvin Amian.
However, after a VAR consultation, the offcial awarded a penalty instead and captain Payet stepped up to beat goalkeeper Baptiste Reynet from the spot.
It was Payet's 68th goal in 352 Ligue 1 games.