Webber was on course for victory but was passed by Vettel during the final stint of the race.
"In the end Seb made his own decisions today and will have protection as usual, and that's the way it goes," Webber said on the podium.
"I was disappointed with the outcome of today's race."
Webber was also caught saying 'Multi 21, Seb' to team mate Vettel in the drivers room before the podium.
"There’s a bit of history to this as well; my mind in the last 15 laps was thinking about a lot of things, but I was happy with the way I drove," Webber added.
"I tried to isolate what happened at the end and we got something out of it today, but of course I’m not satisfied with the result. This puts heat on a few people and unfortunately there’s no rewind button."
Team principal Christian Horner also expressed his disappointment at Vettel.
"Unfortunately drivers’ interests can sometimes come into conflict with the teams’. Sebastian decided to take things into his own hands today and race Mark, thankfully making a clean pass and switching the order to the flag."
"It’s frustrating. Formula One is both a team and an individual sport and sometimes there is a conflict between a driver’s desire and a team’s interest. What happened today is something that shouldn’t have happened. It’s something that Sebastian has apologised for and it’s something that we will discuss internally as a team."