Montpellier have also halted training after a player's partner came into contact with someone who had contracted coronavirus.
The Boks could have used a player of Pienaar's experience and versatility on tour to Europe, and at the Rugby World Cup in Japan next year, but he says that chapter of his career is now firmly closed.
The former Springboks flyhalf fractured his right ankle and will be out for a minimum of 12 weeks just months after his controversial return to French rugby at Montpellier.
Anthony Tuitavake was sent off as Racing 92 lost 23-19 at Agen in the Top 14.
Montpellier have released six players from their contracts, including former Springbok No. 8 Pierre Spies.
La Rochelle climb into Clermont's buffer in the Top 14 standings as Zack Holmes kicks 20 points in 25-19 win over Toulouse.
A Ben Botica penalty three minutes into stoppage time saw Montpellier record a 12-11 victory over La Rochelle.
All the reaction from around the European Champions Cup Round 2 as Toulon got back to winning ways and Munster remembered Anthony Foley.
- MONTP10thTries Scored 1st Clermont Auvergne : 70 Tries ScoredCLER1st3370
- MONTP9thPoints Difference 1st Clermont Auvergne : 232 Points DifferenceCLER1st-2232