Lewis Hamilton and Nico Rosberg topped the times in the morning practice session at the Nurburgring, but it was Vettel who went quickest in the afternoon, beating Rosberg by over two tenths of a second.
Webber, third fastest, suggested Mercedes could prove uncatchable in qualifying trim.
The German squad has been on pole five times in the last six races.
"We are not putting our hopes up for tomorrow," said Webber. "Obviously Mercedes is more than capable of doing a front row lockout which we have seen for the last few races.
"Seb and I look a bit more competitive on one lap today, but Mercedes could put the fuel in.
"We need to keep working hard and it is similar for the race: Mercedes has proved in the last few weeks that it is not slow on Sundays, so there are a few guys that are in contention for the win."
Vettel agreed that his rivals' pace - even over long runs - could prove too strong for Red Bull.
"I think Mercedes was bloody quick this morning, we couldn't have done that," said Vettel. "This morning I was not entirely happy with the car, while in the afternoon I was in better shape.
"The low-fuel run was determined by traffic etc., so we will see - but I am quite happy so far."
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