Nice levelled with a penalty in the 63rd minute, Wylan Cyprien scoring from the spot for the second game in a row after Youcef Atal was fouled by Hamari Traore.
Patrick Vieira's side then took all three points when Coly turned the ball in at the far post after a corner was headed on.
The result left Paris St Germain, Rennes, Nice and Angers all level on nine points from four games with the Parisians leading on goal difference.
In the other afternoon match, Reims converted a penalty awarded after a VAR review that took nearly five minutes on the way to a 2-0 win over 10-man Lille, last season's runners-up.
Reims forward Moussa Doumbia went down under a challenge from Lille captain Jose Fonte in the 68th but play continued and Lille broke down the other end and nearly scored themselves.
The video assistant referee then alerted match referee Eric Wattellier to the Doumbia incident and play was interrupted.
The pitchside monitor was not working so Wattellier had to rely on instructions from the VAR officials, based in Paris, as he finally awarded a penalty which Doumbia netted in the 73rd.
Remi Oudin added a second goal in the 90th with a free kick which appeared to be intended as a cross but which caught out goalkeeper Mike Maignan and flew into the net.
Lille, who played with 10 men from the 53rd minute after Yusuf Yazici was sent off, then squandered a chance to pull a goal back when Jonathan Bamba's penalty was saved by Predrag Rajkovic, who turned the ball onto the post.