Maxwell Cornet and Sergi Darder, with an audacious piece of skill, scored the first-half goals that handed PSG their first Ligue 1 defeat since a 3-2 reverse at Girondins Bordeaux in March 2015.
Laurent Blanc's side are still 23 points clear at the top of the table, after 28 matches, as they sail towards a fourth consecutive title.
"Congratulations to Lyon," PSG defender David Luiz told Canal Plus television. "They played well.
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"We didn't play well tonight and the manager told us to wake
up a bit at halftime but it was too late. We played badly and although we scored a goal, we were tired."
PSG's chances of beating the record unbeaten run of 32 games in a single league season, set by Nantes in 1994-95, were ended despite a Lucas Moura goal after the break.
Lyon have flattered to deceive this season but started strongly and took the lead in the 13th minute when Cornet brought the ball down inside the box, evaded Gregory van der Wiel and slammed the ball past keeper Kevin Trapp.
Darder doubled the advantage in first-half injury time when he received a cross from Rafael, flicked the ball over the head of PSG captain Thiago Silva and finished emphatically.
The visitors were lucky to go in at halftime with 11 men, midfielder Thiago Motta escaping with a yellow card after punching Jordan Ferri in the face in the 23rd minute.
PSG improved after the break when manager Laurent Blanc introduced Javier Pastore for Benjamin Stambouli.
Pastore was quickly influential as his side got back into the game in the 51st minute, the Argentine playmaker tearing into the Lyon box before flicking the ball into the path of Lucas who beat Anthony Lopes with aplomb.
Lyon are third on 42 points, eight behind second-placed Monaco who drew 0-0 at Nantes on Sunday.
Olympique Marseille's match at Ajaccio was postponed due to bad weather while Caen moved above Nice into fourth spot after securing a 2-1 victory at St Etienne whose European aspirations have been dented after going three games without a win.
(Writing by Ed Dove, editing by Ian Chadband)
