Lorient's Alain Traore struck in the 91st minute and Jeremie Aliadiere's cool finish deep into stoppage time sealed a special win for the Britanny side, who almost beat title favourites Paris Saint-Germain last weekend before a late draw.
Montpellier's Argentine striker Emanuel Herrara, bought from Chile's Union Espanola as a replacement for new Arsenal frontman Olivier Giroud, had netted his first French league goal after 37 minutes following good work from John Utaka.
The south coast side, who stunned French football by beating big-spending PSG to last term's title despite a modest budget, drew last week's season opener 1-1 with Toulouse.
Lyon had started with a 1-0 win at Stade Rennes and followed that up with a 4-1 home romp over Troyes, with tall striker Bafetimbi Gomis scoring at the start and end of the second half with a fierce header and a powerful finish.
The hosts had gone one down and missed a penalty before rattling off four goals in the second half, including a superb overhead kick by Brazil's Michel Bastos.
"We have started well. We did some interesting things with the ball but there are still situations where we need to do better and which we need to work on," coach Remi Garde told reporters.
Late on Garde introduced new Serbian defender Milan Bisevac, who joined from PSG in midweek in a deal which was meant to see Anthony Reveillere go the other way only for the France international to fail a medical and stay at Lyon.
The only downside for Garde's side, champions every season from 2002 to 2008 before a lean spell, was an early knee injury to playmaker Yoann Gourcuff.
In Saturday's other matches, Toulouse beat Saint-Etienne 2-1 at home, Stade Brest overcame Evian 1-0, Valenciennes drew 0-0 with Nice and Bastia got past fellow promoted side Stade de Reims 2-1 in Corsica thanks to Brazilian Ilan's injury-time strike.
Lille, the 2011 champions, drew 1-1 at home with Nancy on Friday.
