Maxwell Cornet controlled Alexandre Lacazette's pass to drive in an opener.
Sergi Darder added an exquisite second on half-time, controlling Rafael's cross and flicking it past Kevin Trapp.
Despite Lucas Moura's steered finish, PSG lost their first league game since last March, but still have a 23-point lead at the top.
Laurent Blanc's side had not lost a league match since a 3-2 defeat at Bordeaux 11 months earlier, but looked off the pace and struggled without the creative influence of injured winger Angel di Maria.
After Cornet's opener, PSG could have been reduced to 10 men, as midfielder Thiago Motta escaped with a booking for raising his fist to the side of Jordan Ferri's head.
The leaders' best spell of pressure came shortly before Darder made it 2-0, with Zlatan Ibrahimovic having a shot beaten out by Lyon keeper Anthony Lopes.
PSG rarely looked like equalising after Lucas scored, and the excellent Rachid Ghezzal should have added a third for the home side when clean through, but Trapp advanced from his line to block.
Monaco, in second place, end the weekend having narrowed the gap at the top, despite dropping points themselves in a 0-0 draw at Nantes.
Caen had moved above Lyon and into third earlier on Sunday by winning 2-1 at St-Etienne, with former Wigan striker Andy Delort among the scorers.

It relates to Vodafone's 2007 takeover of Hong Kong-based Hutchison Whampoa's Indian mobile unit for $11bn (Â£6.5bn).
Indian authorities have said the firm owes nearly $2.2bn in taxes over the deal, a claim the firm has disputed.
India's top court ruled in favour of Vodafone in 2012, but the government changed laws later that year to allow firms to be taxed retrospectively.
That development was criticised by investors and also triggered concerns among many foreign firms looking to enter India.
Vodafone's Dutch subsidiary acquired a 67% stake in CGP Investments Ltd, a Cayman Islands registered company which held the Indian telecom assets of Hutchison in May 2007.
Vodafone has long claimed that the deal was not subject to any taxes in India as the assets were held by a firm based in the Cayman Islands.
However, the Indian authorities presented it with a tax demand of 112bn rupees - equivalent $2.2bn at the time.
The Indian government subsequently also sought penalties of up to 100% of the original bill.

It launched a scheme for 500 UK teenagers amid looming staff shortages, with the Guardian reporting the young people would only get free food.
But following online criticism, the sandwich chain said it would pay participants and give them free food.
The firm said it saw "how passionately people feel about the initiative".
One in 50 Pret applicants is British
The company launched its Big Experience Week after it said it would struggle to staff its outlets following Brexit because just one in 50 job applicants is British.
Its director of human resources, Andrea Wareham, said UK job seekers did not see it as a desirable place to work.
The Big Experience Week would give participants exposure to aspects of its business, including food production, customer service, "social responsibility" - described as care for the homeless - and financial control, Pret said.
However, following criticism on social media that the placements would be unpaid, the company tweeted a statement saying it would now be paying participants.
Pret CEO Clive Schee said: "Pret's work experience week is not about making sandwiches for free.
"We set it up so that 16-18-year-olds can shadow our teams and get a flavour of what working at Pret is like.
"We've seen how passionately people feel about the initiative, and in response I would like to confirm that we will pay all participants."
A spokeswoman for the company added that the teenagers were "not there to work themselves" and would instead be shadowing team members.
Paris St-Germain's 36-match unbeaten run in Ligue 1 was ended as Lyon beat them to move into the third and final Champions League qualification spot.
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Vodafone has sought international arbitration to resolve its tax dispute with the Indian government.
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Pret A Manger has said it will pay teenagers on a week's work experience its starting hourly rate after reports it planned to "pay them in sandwiches".