The Spanish midfielder nodded PSG in front at the Parc des Princes on 19 minutes and then fired in a second from close range on the half-hour.
Kylian Mbappe, who shook off a calf injury picked up on international duty with France, raced clear of the Clermont defence to add PSG’s third before Idrissa Gueye headed in a fourth.
Mauricio Pochettino’s team made it five wins from five in Ligue 1, stretching their lead to five points over Angers, who take on struggling Brest on Sunday.
Pochettino left Argentina duo Messi and Angel Di Maria, and Brazil star Neymar out of the squad to allow them extra time to recover ahead of Wednesday’s Champions League opener at Club Brugge.
“They arrived yesterday (Friday) afternoon and they trained today. They’re tired from the trip but I’m happy they came back in good shape, without physical issues, to be there for the Champions League,” said Pochettino.
The trio were all involved in qualifiers in South America on Thursday, with Messi’s home debut for PSG pushed back after his record-setting hat-trick against Bolivia.
The triple strike made Messi the top international goalscorer in South American football history with 79 goals, overtaking Pele.
Clermont, playing in the top flight for the first time, entered the weekend a surprising third, and unbeaten after two wins and two draws.
But the visitors were without forward Mohamed Bayo, the Guinea striker ruled out of the game after the coup d’etat in the African country delayed his return to France.
Supporters had jeered when Mbappe’s name was read out by the stadium announcer ahead of kick-off last month against Strasbourg as speculation mounted over a potential move to Real Madrid.
Having stayed put, Mbappe will spend the rest of the season in Paris. However a smattering of pre-match whistles still greeted the player whose contract expires at the end of the campaign.
“I didn’t hear anything. If it happened, I didn’t see or hear it,” said Pochettino.
“Kylian is a great professional, a tremendous player and a good person. He loves the club, he’s showed that all these years and he continues to do so.
“He tries to get better each day and help the team achieve its targets.”
Italy goalkeeper Gianluigi Donnarumma made his first start for PSG since signing from AC Milan, but it was another summer arrival, Achraf Hakimi, who created the opening goal.
The Moroccan wing-back’s fierce low ball across the box was palmed out by Arthur Desmas, leaving Herrera to head home with the Clermont goalkeeper stranded.
PSG’s second goal came in similar fashion as Mbappe’s delivery was only partly cut out by Clermont captain Florent Ogier, presenting Herrera with the simplest of chances.
Mbappe notched his fourth goal of the season 10 minutes into the second half as he ran onto Julian Draxler’s ball over the Clermont defence and rounded Desmas to slot in.
The France striker played a central role in PSG’s fourth of the afternoon as well, drawing a fine save from Desmas before the rebound looped towards Gueye, who stooped to nod into an empty net.
Senegalese forward Bamba Dieng grabbed both goals for Marseille in a 2-0 victory away to Monaco as Jorge Sampaoli’s side stayed five points back of PSG with a game in hand.
Monaco have lost three of five games to the start the domestic season, having also fallen in qualifying for the Champions League.