While George Russell grabbed fourth on the grid thanks to Lando Norris' error and Sergio Perez's best time being deleted, Mercedes are at risk of losing second place in the F1 Constructors' Championship after Charles Leclerc put his Ferrari on the front row.
There is little left to fight for at the final race of the 2023 season and it was little surprise to see world champion Max Verstappen grab pole position.
"Very weird, the whole weekend has been a bit of a struggle," stated the Red Bull driver. "From lap one it seemed a bit more together and we could push more."
Leclerc was just over a tenth behind in second ahead of Oscar Piastri as McLaren continued their strong finish to the season.
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"Difficult session, it's extremely tight this weekend," said the Australian rookie. "A bit of a messy one, pace has been there but a lot of mistakes. Happy with that, nice turnaround from Vegas for us."
Yas Marina Circuit provided plenty of shocks with drivers struggling to warm their tyres up and traffic prevalent in the late stages of each session.
Hamilton was knocked out in Q2 by just 0.081 seconds and complained of a lack of grip in his Mercedes, with replays showing the seven-time champion fighting his steering wheel in the last sector.
"There's something not right with this car," he told team radio while trundling back to the pits.
Carlos Sainz will start near the back of the grid after bad traffic restricted his Ferrari to 16th and a surprise Q1 knockout to continue a bad-luck end to the season for the Spaniard.
Ferrari sit four points behind Mercedes in the Constructors' while Sainz, Fernando Alonso, Norris and Leclerc are involved in a fight for fourth in the Drivers' Championship.