Bottas clocked a best lap in one minute and 36.276 seconds to outpace Hamilton, back after a bout of Covid-19 that forced him to miss an F1 race for the first time, by 0.203 seconds.
"Mega, mega lap", team boss Christian Horner told Verstappen on the radio.
Hamilton said: "Honestly, really grateful be back here with the team and try to close out the strong season we've had".
Hamilton indicated on Friday that the Brackley-based team, who this year wrapped up a record seventh straight title double, could use Saturday's hour-long session to run their cars on higher fuel loads, suggesting normal order could be restored come qualifying.
"I gave it my all, congrats to Max".
"It is always nice to start first but this makes it even more exciting". "I am definitely excited to see how I can turn it around".
Hamilton said he gave it his best, following his illness.
But with Mercedes, who have been on pole in Abu Dhabi every year since 2014, believed to be running their cars on a heavier fuel load, normal service was expected to resume for qualifying.
"He will need to kick me quite hard in a sensitive zone for me to ever lose my morality and I am loyal to my two race drivers in the same way I am loyal to my two junior drivers".
"I don't want to go into too much detail of the experience", said a noticeably slimmer Hamilton, who coughed on several occasions during his post-qualifying media duties. Ricciardo is competing in his last race for Renault before joining McLaren next year and has two third-place finishes this season. But he does not have a seat for next year after being replaced by Vettel, when Racing Point is renamed Aston Martin following a takeover.
After his standout driver last weekend at Sakhir where a rare Mercedes pit stop blunder squandered his chances of clinching a sensational maiden win in F1, Russell is waiting on whether Lewis Hamilton will get a clean bill of health and return to Mercedes for F1's season finale.
Max Verstappen was third for Red Bull, seven-tenths adrift, at the end of a session that began and finished with tyre-testing and was also interrupted by a red-flag period after Kimi Raikkonen's Alfa Romeo's Ferrari engine burst into flames.