Following PSG's slip-up at home to Ajaccio on Friday evening, Les Gones had youth-team products Maxime Gonalons and Samuel Umtiti to thank for the goals that took them three points clear of Marseille and ahead of the Parisians.
The hosts made a lively start. Stephane Darbion tested Remi Vercoutre with a stinging left-footed volley after the winger combined well with Corentin Jean.
Minutes later the referee waved away Troyes' penalty claims after Bafetimbi Gomis appeared to handle the ball in the area following a corner.
In a frenetic opening quarter of an hour Michel Bastos created the first opportunity for the visitors - his left-footed free-kick from distance forcing Yohan Thuram into a superb two-handed save.
Lyon took the lead after 11 minutes. New captain Gonalons met a Steed Malbranque corner at the near post and nodded the ball beyond Thuram.
Troyes reacted and in the 25th minute Darbion saw his shot turned away by Vercoutre only for Jean to turn a cross over the bar from close range with the goal at his mercy.
However, their efforts paid off before half-time. Julien Faussurier attacked down the right before delivering towards Benjamin Nivet who despatched a sublime left-footed volley which crashed against the bar and nestled in the back of the net.
Troyes started the second half like they did the first. The lively Benjamin Nivet fired wide from inside the area after being set up by Jean. Shortly after Granddi N'Goyi met a Stephane Darbion free-kick but his header was gathered comfortably by Remy Vercoutre.
Following a quiet period in play, Lyon made three substitutions in the space of five minutes in an effort to swing the game their way.
The change paid off in the 76th minute when Umtiti put his team back in front.
Following Arnold Mvuemba's corner, the young French defender saw his initial effort cleared off the line by Fabien Camus.
But he was given a second opportunity when the clearance fell back at his feet and made no mistake, firing home with his left foot.