The Renault driver, 26, was four seconds slower than Verstappen's best effort and an eye-watering 1.3secs adrift of team-mate Nico Hulkenberg, who has out-qualified the Englishman at every round of the campaign so far.
Red Bull's Max Verstappen led the way in both practice sessions for the Azerbaijan Formula One Grand Prix but has left his mechanics with plenty of work to do after crashing.
Daniel Ricciardo finished the morning session second on the timesheets, nearly half a second down on his team-mate, while championship leader Sebastian Vettel was third in his Ferrari.
"It was very weird to be honest, I locked up and was still trying to make the corner, but I tried to play it safe and take the exit road", he explained to Sky F1. "I locked up and I was still trying to make the corner and then I made a decision to play it safe and take the exit road".
"Suddenly I lost the rear and then I just had a four-wheel power slide into the barrier".
It was a scrappy day punctuated by several misjudgements on the scorching Baku circuit.
The Brit will be eager to enhance his title credentials by becoming the first driver to win successive races this season at this weekend's race at the Baku City Circuit.
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Vettel got down to 1m 44.957s on softs to go third, leaving Hamilton fifth on his soft-tyre time and Bottas sixth after he had moved the second Mercedes up to 1m 45.737s on the supersoft tyre.
"I think the circuit is definitely as tight as it looks and has a lot of corners, unlike any others on the calendar", Ricciardo said. I think I used reverse three times and I haven't used reverse once in the last three years but it is good to do this today so we don't have to tomorrow.
Bottas, who set that top speed of 370 kph (230 mph) in last year's inaugural race, struggled on Turn 10 and barely managed to avoid any contact with the barriers.
Hamilton recorded the best time in each of the three practice sessions in Baku past year, before a crash in qualifying ruined his chances of success.
The second practice starts late Friday afternoon.
"I think you need to get into a rhythm in Baku, do laps to gain confidence and have the tyres in the right window", said Mercedes boss Toto Wolff. In the second session I felt I couldn't get the maximum out of the short run pace due to yellow flags and traffic so we can be very happy to still finish P1.
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