Ibrahimovic bundled in the opening goal just past the hour at the Parc des Princes, and the Swede added a second soon after as PSG began to turn the screw.
Adrien Rabiot then netted a third on 75 minutes, with Laurent Blanc's men staying firmly on course to repeat last year's domestic treble.
Blanc handed Edinson Cavani, relegated to several substitute appearances in Ligue 1 since the turn of the year, a start in place of Angel Di Maria, while midfielder Blaise Matuidi made way for Benjamin Stambouli in midfield.
A quiet first half saw Paris fail to register a single shot on target, with Cavani wasting the home side's best opportunity when he steered wide after Lucas picked out the Uruguayan just inside the area.
Maxwell Cornet went close to giving Lyon the lead five minutes before the break, but Salvatore Sirigu flung himself to his left to brilliantly turn behind the teenager's curling effort.
Ibrahimovic drilled narrowly wide early in the second period, but PSG's mounting pressure eventually told on 63 minutes as Lucas burst down the left-hand side before crossing for Ibrahimovic to chest home.
The Swede struck again just four minutes later when Serge Aurier slid in a low cross from the right for Ibrahimovic, who was marginally offside, to poke beyond Anthony Lopes.
Alexandre Lacazette blazed over as Bruno Genesio's men sought to reduce the deficit, and the visitors were understandably aggrieved when Rabiot, clearly behind the last defender, converted Maxwell's left-wing cross to seal a fourth win in as many attempts over Lyon this season.
Earlier, Nantes came from behind in extra time to claim a thrilling 4-3 victory at Bordeaux, with US international Alejandro Bedoya netting a 118th-minute winner.
Saint-Etienne also needed extra time to see off Ligue 1's bottom side Troyes as France Under-21 forward Neal Maupay struck the decisive blow in the 107th minute, while Lorient thumped fourth-tier Sarre-Union 4-0.
On Tuesday, second-division strugglers Sochaux knocked out Monaco with a 2-1 victory at the Stade Auguste Bonal, with Gazelec Ajaccio and fifth-tier Granville also advancing.
However, Granville goalkeeper Clement Daoudou was hospitalised following an assault at a fast-food restaurant after the match, which left him with heavy bruising and a broken nose.
"We're shocked and outraged by what happened. It was in no case a fight but indeed an assault," Granville's co-president Fabrice Clement was quoted as saying by regional daily Ouest France.