PSG made the most of Timothee Kolodziejczak's red card on the stroke of halftime as Messi fed Marquinhos for two headed goals and Angel Di Maria struck to seal a clinical turnaround after Les Verts had opened the scoring through Denis Bouanga.
The result put the capital side on 40 points from 15 games, with third-placed Rennes having a chance to leapfrog Nice into second when they travel to Lorient later on Sunday.
St Etienne, who mounted on a decent challenge despite being a man down as snow fell on the Geoffroy Guichard stadium, are now bottom of the standings with 12 points.
The game marked Sergio Ramos's debut for PSG, almost five months after joining from Real Madrid as a free agent, and the Spaniard started in central defence alongside Marquinhos.
St Etienne pressed high and PSG looked to hit them on the break, with Neymar finding the back of the net early on only for the Brazilian's goal to be ruled out for offside.
The hosts went ahead after 24 minutes when Kolodziejczak, set up by a superb Wahbi Khazri through pass, shot straight at goalkeeper Gianluigi Donnarumma but Banga followed up and fired home from point-blank range.
The momentum, however, swung towards PSG in a couple of minutes on the stroke of halftime.
Kolodziejczak was harshly shown a straight red card for bringing down Kylian Mbappe as the France striker charged towards goal and Marquinhos headed home Messi's perfectly-executed free kick.
Messi was at it again 11 minutes from time, whipping a fine pass behind the back of the defence for Di Maria, who finished with a curled effort into the far corner of the net.
Marquinhos headed home again from Messi's cross in the last minute, three minutes after Neymar was carried off after twisting his ankle.