Sebastian Vettel was sure Mercedes was sandbagging ahead of qualifying for the Singapore Grand Prix after the team struggled for the first time this year.
Teammate Nico Rosberg finished sixth.
Hamilton had scored 11 poles in 12 races, and seven in a row until Singapore.
Vettel, however, says he is expecting Mercedes to fight back on Sunday.
"We don't mind, Sorry! I don't know, it is a surprise," said Vettel of Mercedes's performance.
"I thought yesterday they were sandbagging and this morning.
"No doubt they have the strongest package this year, they have a very good car, a very good power unit.
"They must have some issues and are not feeling comfortable at all. I wouldn't rule them out for tomorrow. It's not the easiest circuit to overtake but if you have the pace you come through.
"I expect them to come through."
Near perfect lap
The Ferrari driver, who beat his closest rival Daniel Ricciardo by half a second, was impressed by his own flying lap.
"I had a proper one I would say! Unbelievable," he added. "This morning, to be fair, the car was fantastic to drive. It got better through qualifying, we did the maximum today.
"I was surprised by the margin but I think it came together. I had a near perfect lap at the end."
Teammate Kimi Raikkonen qualified in third, over seventh tenths behind Vettel.