Finnish team mate Valtteri Bottas, who had gone top moments earlier, had to settle for second - just 0.118 of a second slower - as the Silver Arrows locked out the front row in style.
Both suffered comprehensive damage to their cars and had to retire, leaving Romain Grosjean to carry the French flag after surviving an incident when Vettel, minus a front wing on his Ferrari, made contact with his Haas vehicle.
Red Bull's Daniel Ricciardo has won two races this season and needs to start adding to that tally soon to have any chance to stay in contention for the drivers' championship.
Hamilton lost his lead in the standings to Vettel two weeks ago when Mercedes couldn't deliver a planned engine upgrade on time. "I got a great response from the crowd and I'm delighted to be here for the first time", Hamilton said to reporters.
"My start was too good".
"After that it was hard as the vehicle was quite damaged and I could feel the lack of rear end".
Hamilton's main challenger for the fastest time at the Paul Ricard Circuit was teammate Valtteri Bottas, who was the second quickest ahead of points leader Sebastian Vettel in his Ferrari.
Asked if it felt like the team was suffering a downturn in performance, Alonso said it was better to wait for race day after a series of strong results on Sundays this season.
"We need to identify the cause of the water leak, but we're confident that we continue to run the new engine." . The guys did a great job.
Bottas, with a punctured rear left tyre, and Vettel managed to steer their damaged machines back to the pits for repairs and rejoined the fray at the back of the field. "Obviously today, I would have loved to have a different result but we move on". "He destroyed the whole race for himself and for Bottas". "We're all on the edge, we're fighting for the world championships, we're not pootling around, we're out there putting our lives on the line, we're out there putting the cars as far beyond the edge as we can in the safest manner. We are not twiddling around".
A threat of rain appeared to be developing before easing, but it did send the race into a little lull as drivers tried to look after their tyres to make them last in case the weather did turn. "From there, obviously we had a good recovery but it wasn't the race we wanted".
Lance Stroll also failed to finish when a tire blew on his Williams.
Basking in the Mediterranean sun, driving conditions were optimal at the 5.8-kilometre circuit situated next to a private airport where planes took off and landed all weekend.