The teenager became the first player in Europe's top five leagues to reach 10 goals this season to seal all three points and cement the defending champion's place at the top of Ligue 1.
Thomas Tuchel's side restored an eight-point gap over second-place Lille after an 11th league win in a row, confirmed by Julian Draxler's stoppage-time finish, that equals the record start to a campaign set by Tottenham Hotspur 58 years ago.
PSG's surprising 3-5-1-1 set-up did little to unsettle the Marseille defence in the first half, in which the only major chance of note occurred in stoppage-time, when Kevin Strootman cleared Angel Di Maria's shot off the line.
It took less than a minute of the second half for Di Maria to force Steve Mandanda into his first save of the match, the keeper parrying a bouncing shot past his left-hand post.
Neymar had been targeted by missiles thrown from the crowd throughout, but he nearly silenced the home fans with a low left-footed drive after a dazzling run into the penalty area.
Opposite number 10 Dimitri Payet had a similarly quiet game, although he tested Alphonse Areola with a free-kick, before Tuchel turned to Mbappe in the 62nd minute to try to ignite a spark in his attack.
It did not take long. PSG won back possession in their half, Di Maria quickly sent Mbappe forward on the break and the attacker held off Boubacar Kamara to drill past Mandanda.
Thomas Meunier was denied a second by Mandanda and Jordan Amavi shaved the outside of the upright, but PSG secured the win with practically the last kick of the game, Draxler sliding in to score after Neymar had scuffed Mbappe's pass across goal.
Next up for PSG is the visit of Lille to the capital, before a key UEFA Champions League clash with Napoli just four days later.
Marseille travels to Montpellier in a week and then turns its attentions to its own trip to Italy, where it will face Lazio in the UEFA Europa League.