Ferrari's Sebastian Vettel will start second place with Red Bull's Max Verstappen at third and Charles Leclerc of Ferrari at fourth.
Valtteri Bottas put pen to paper a one-year contract with an extension option for 2020, which Mercedes have exercised.
Bottas, who leads Hamilton by one point in the standings, got back out with 15 minutes left of the session and clocked the third fastest time.
That was the fourth straight one-two finish for Mercedes, the best start to a season by a two-car team in Formula One history.
Mercedes driver Valtteri Bottas had vowed to come back stronger this year after flopping for much of 2018.
The 29-year-old Finn kept his emotions in check after what he described as the drive of his life to win the Australian GP on Sunday, his fourth F1 title and his first since 2017.
Mercedes was a hot favourite to win in Melbourne after dominating every practice session but surprisingly, it was Bottas who finished with a gap of 20 seconds.
Bottas competed with Hamilton on occasions last season but a mixture of bad luck, tentativeness and team orders saw him finish the year with seven second-place finishes and no wins.
Starting from pole, the Mercedes driver was never seriously challenged and crossed the finish line 12.919 seconds ahead of teammate Valtteri Bottas.
Bottas was 0.145 ahead of Hamilton and 0.56 ahead of third-placed Sebastian Vettel, who is second in the standings, 40 points off Hamilton.
Bottas moved from Williams on a one-year deal as an emergency replacement for German driver Nico Rosberg, who stunned Mercedes — and all of F1 — by retiring days after winning the 2016 title.
Hamilton, who is going for a fifth straight victory and a record sixth overall in his home Formula One race, clocked the best lap time at 0.367 seconds faster than Bottas.
Bottas edged Hamilton by 0.019 seconds for his first pole position of the season as Mercedes locked up the front row of the grid for the third time this year.
Ferrari's Sebastian Vettel, who trails Hamilton by 14 points going into Sunday's ninth of 21 races, had a fastest lap that was 0.236 behind Hamilton's.
Heavy rain kept drivers in the garage for most of the final practice of the French GP with Valtteri Bottas of Mercedes ending up fastest in the washed-out third session.
The last time an F1 race was held here at Le Castellet was in 1990 when Alain Prost won for Ferrari.
Valtteri Bottas is urging Mercedes teammate Lewis Hamilton to sign a new contract, even though his own future is uncertain with the team.
Hamilton had a time of 1 minute 17.281 seconds at the Circuit de Barcelona-Catalunya, with Bottas less than a tenth of a second slower.
Ferrari's Sebastian Vettel, who trails Hamilton by four points in the drivers' standings after four races, was third.
The Mercedes duo of Valtteri Bottas — fastest in the first session — and defending champion Lewis Hamilton ranked fourth and fifth, respectively, in the second practice.
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