The Europcar rider, in his first year as a road pro, took advantage of a crash inside the final kilometre to lead home Francesco Chicchi (Vini Fantini–Selle Italia) and Allan Davis (Orica GreenEdge) at the conclusion of a 123.6km stage from Pasir Puteh to Kuala Berang.
Astana's Andrea Guardini, who holds the points jersey, struggled with illness. Six members of the peloton were struck down with suspected foot poisoning, leaving Davis's Australian squad with only three riders.
It is 20-year-old Coquard's fourth win of 2013.
"It's very good, it's amazing and just very happy for Team Europcar," said Coquard. "There was a crash, I was lucky to avoid it and after Kevin Reza launched me perfect into third position for the sprint.
"I was behind [Graeme] Brown and Davis. At 200m I opened up my sprint."
Coquard, who previously won two stages at the Etoile des Bessegges and took silver for France in the London 2012 Omnium, said his success in track cycling gives him a good grounding to contest the sprints.
"The track is a better school for sprinters I think because I am very [skilled] on the bike," he added.
Julian Arredondo (Team Nippo–De Rosa) looks likely to win the GC on Saturday's final stage after again coming home in the lead group on a stage which again saw occasional showers.
"I'm very happy. I hope for a bunch sprint finish again tomorrow," he said. "That would confirm me as the champion of the Tour de Langkawi."
There were no early breakaways, with Chicchi taking the first intermediate sprint. The Vini Fantini–Selle Italia would share the sprint spoils with points jersey holder Andrea Guardini (Astana), who seemed to be struggling with illness. Six members of the peloton were struck down with suspected foot poisoning, leaving Davis's Australian squad with only three riders.
Chinese Meiyin Wang (Hengxiang) looks likely to win the King of the Mountains as team-mate Yilin Liu, who led a two-man breakaway on the second half of the stage - which build a maximum lead of two minutes - took the points atop the Cat 4 climb at 77km.
Liu then left Endra Wijaya (Indonesia National Team) and went out alone, only to be caught by the bunch with 20km remaining.
"We decided that if someone could take the points, then they could go," said Wang. "I can now be relaxed in the bunch tomorrow."