The Frenchman had been in the running to become Sebastian Vettel's team-mate in 2014, but the fight for the second Red Bull seat is now effectively between Daniel Ricciardo and Kimi Raikkonen.
Although losing out on the Red Bull opportunity will be a disappointment, Vergne's team boss Franz Tost says there is no doubt that he can keep his current seat for next year.
"I'm convinced that Jean-Eric Vergne will race next year for Toro Rosso," said Tost ahead of the Hungarian Grand Prix.
"We must not forget that Jean-Eric came later into F1 [than Ricciardo] and why Red Bull Racing is thinking about racing with Daniel Ricciardo next year, it's simply because he is more experienced, he showed very good performance in the first half of the season.
"But Jean-Eric Vergne is quite close to him. It's not that Jean-Eric is out of the team. As far as I'm thinking, next year he is with Toro Rosso."
Ricciardo's performance for Red Bull in last week's young driver test was praised by team chiefs, and Tost said he would have no complaints if he lost the Australian to the senior team for 2014.
"We will see. It's not decided yet from Red Bull but we must not forget Dietrich Mateschitz and Red Bull bought Minardi in those days to give young drivers from the Red Bull driver pool a chance to come into F1," he said.
"Toro Rosso is the team to educate young drivers and I see it as positive because it shows that a) drivers are skilled and b) that the team has done so far a good job. Therefore if they choose Daniel I am quite happy with this decision."
VERGNE CONTENT TO STAY
Vergne is happy to stay at Toro Rosso in 2014, even though he feels that he would be ready for promotion to Red Bull.
He is confident that the team will be able to take a step forward next season and backed it to do so.
"I would be really happy to stay with Toro Rosso next year," said Vergne.
"Of course, it would be a dream to go and drive for Red Bull Racing but I really believe in the team [Toro Rosso], especially the people working in the team.
"They are putting a lot of effort into next year's car and I really believe that we can have a good season next year and that the car will be much better than the one we have now."