As team-mate Nico Rosberg surged to a surprise pole position, Hamilton was 0.432 seconds adrift in fourth place. He is also due to get a five-place penalty for having a gearbox change prior to qualifying.
Hamilton had been unhappy with his car on Friday, but felt he made a breakthrough on Saturday morning, only for that pace to fade away again.
"The car didn't feel the same as it did in P3," said Hamilton. "The guys are looking into the data.
"P3 was a big improvement. P1 and P2 we had some problems with the car and fixed it overnight.
"But we got to qualifying and it felt like it did yesterday.
"Whatever it was, it doesn't matter. Nico did a great job today. I wasn't able to match his pace.
"Tomorrow's going to be a tough race from ninth place but I'll do what I can."
Hamilton incurred his penalty when his gearbox was among the components damaged by a blown tyre at the end of practice three. Pirelli believes debris was to blame.
"The rules are the rules. I just have to suck it up and deal with it," said Hamilton.
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