The McLaren driver failed to leave enough time to start a second fastest lap of the session.
"It was my mistake," said the 26-year-old. "I should have got out sooner but I was making a wing change and I went out too late.
"The team were telling me when I need to get a lap but it was not the team's decision, so it was my fault."
Hamilton had set the benchmark during the final phase of qualifying, but was eventually beaten by Vettel and teammate Jenson Button and will now start tomorrow's race in third position.