Webber was leading the race ahead of Vettel following the fourth and final pit stop and although the team ordered the pair to be cautious, they went wheel to wheel, with the German overtaking his team-mate to take the win.
Webber was visibly angry following the race with Vettel admitting: "I made a big mistake."
Ecclestone, however, saw it differently.
"At this stage of the championship, I do not believe there should be any team orders. It does not matter who it is," he told the Daily Telegraph.
"Let's assume that these two guys are in a position to win the championship at the end of the year, then there is no way that Mark is going to help Sebastian.
"So Sebastian has to think about that. Maybe there will be a stage when he would like Mark to help him, but I don't think Mark is going to come up front and do it.
"When you are three-quarters of the way through the year, then it's important. If there is only one guy who could get enough points to win the title, then the other guy should be helping him, for sure."
Lewis Hamilton finished the race third, with Mercedes team-mate Nico Rosberg fourth, after the team ordered the German not to pass, despite being quicker than the Brit.
"You shouldn't have that, should you?" Ecclestone added.
"I was disappointed that Mercedes didn't let Rosberg go past. I thought that was a stupid decision. I think Rosberg could have chased the two Red Bulls down a little more. That decision wasn't sensible."