Toulouse's contrasting home and away form continued as they defeated visitors and 2018-19 Top 14 final opponents Clermont Auvergne.
An early red card was decisive as Bordeaux-Begles suffered their second defeat of the Top 14 season.
Kylan Hamdaoui scored late as Top 14 strugglers Stade Francais edged out Toulon, while Bordeaux-Begles ran riot against Clermont Auvergne.
Racing 92 dominated the second half to beat Pau before La Rochelle were beaten by Toulon at Stade Mayol.
Despite seeing their try line breached for the first time this season, Lyon maintained a 100 per cent start to the season in the Top 14.
Toulon and Agen each won in the Top 14 on Sunday, with Racing 92 unable to complete a turnaround while Montpellier were outplayed.
The second round of Top 14 fixtures saw hard-fought wins for Clermont Auvergne, La Rochelle and Montpellier, among others, on Saturday.
There were shock wins for Bayonne and Bordeaux-Begles as the Top 14 returned for the 2019-20 season on Saturday.
England international Ben Te'o has joined Toulon until November to provide cover for players leaving the Top 14 side for the World Cup.
There will be a new Top 14 champion after Castres missed out on a top-six finish with a final-day defeat to Toulon.