It continued the French World Cup winners’ strong start to the season after a summer marred by a high-profile contract dispute.
Achraf Hakimi and Marco Asensio also got on the scoresheet as PSG effectively wrapped up victory with all four first-half goals at the Groupama Stadium.
Corentin Tolisso gave the hosts a second-half consolation but the result came under pressure under Lyon manager Laurent Blanc’s fire.
Blanc’s side are now bottom of the table with just one point from four games and were booed at half-time and at the end of the match.
In contrast, Mbappe is experiencing a turnaround in fortunes. After months of headlines and speculation about his future, the forward has let his football do the talking in recent weeks.
The 24-year-old has scored three goals in his first two games of the season and netted another after just four minutes after PSG were awarded an early penalty.
Tolisso was at fault when he brought down Manuel Ugarte and Mbappe made no mistake at the spot.
Rayan Cherki fired wide at the other end but Vitinha and Mbappe went close for PSG’s second before Hakimi doubled the lead when he pounced on the rebound after 20 minutes.
Duje Caleta-Car and Cherki had chances as Lyon responded but Hakimi hit the crossbar for PSG and the visitors took firm control when Ugarte equalized for Asensio’s third seven minutes before the break.
PSG weren’t done there as a quick break led to Asensio releasing Mbappe and the forward produced some brilliant football to score his second in the first half through injury time.
Lyon were booed at the break and almost got worse after the restart when Ousmane Dembele’s looping header hit the crossbar.
The visitors pulled one back when Warren Zaire-Emery brought down Nicolas Tagliafico and Tolisso converted the resulting penalty in the 74th minute, but the result was never to change.
PSG eased up in the latter stages as they wrapped up a comfortable victory.
Mbappe had a chance to complete a hat-trick in injury time but fired the ball into the side netting.