Hamilton started on pole for this weekend's Belgian GP but fell back to third in the race as Vettel dominated and Fernando Alonso fought up from ninth to second for Ferrari.
Mercedes had been off the pace through practice before Hamilton took advantage of the wet conditions in qualifying to snatch pole.
He admitted that Mercedes' lower-downforce package underperformed.
"Every year you come here and to Monza with a new package, and sometimes you hit the nail on the head and sometimes you don't," Hamilton said.
"I think we have done a decent job but these guys [Red Bull and Ferrari] have done a better job.
"Whether or not we'll have done an adjustment for the next race, we have to wait and see, but I think we will be more competitive when we get back to Singapore.
"I feel we have much more chance there."
Hamilton said there was little he could do about Vettel and Alonso in the race at Spa.
"I got a decent exit out of the first corner Vettel was massively fast through Eau Rouge, I came out of there and couldn't do anything and had to watch him ride by," said Hamilton.
"After that it was very difficult to hold on and Fernando flew by me on the straight."
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