Asked whether the project could still happen after the exits, Agnelli told Reuters: "To be frank and honest no, evidently that is not the case."
Twelve of Europe's leading football clubs -- Juve, Inter Milan, AC Milan, Real Madrid, Barcelona, Atletico Madrid, Manchester United, Manchester City, Liverpool, Chelsea, Tottenham Hotspur and Arsenal -- announced a breakaway league on Sunday but after 48 hours of intense criticism and political opposition, the six English clubs backed out on Tuesday.
Agnelli said he remained convinced that European football needed change and he had no regrets about the way the breakaway attempt was made.
"I remain convinced of the beauty of that project," Agnelli said, stating it would have created the best competition in the world.
"But admittedly ... I mean, I don't think that that project is now still up and running," he said.
Agnelli's comments were followed up by a statement from Juventus later on Wednesday, echoing his commitment to the idea of a Super League but accepting it could not happen in the form originally announced.
"With reference to the press release published by Juventus Football Club on April 19, relating to the proposed creation of the Super League, and the ensuing public debate, the issuer clarifies to be aware of the request and intentions otherwise expressed by certain clubs to withdraw from this project, although the necessary procedures envisaged by the agreement among the clubs have not been completed," the statement said.
"In this context, while Juventus remains convinced of the soundness of the project's sport, commercial and legal premises, it believes that at present there are limited chances that the project be completed in the form originally conceived.
"Juventus remains committed to pursuing the creation of long-term value for the company and the entire football industry."
Chelsea were the first team to begin the process of withdrawing from the league as fans gathered outside Stamford Bridge ahead of their came against Brighton. They were quickly followed by City and then the four remaining Premier League teams.
Liverpool owner John W. Henry released a formal apology to fans on Wednesday over how the club joining the league was handled.
"It goes without saying but should be said that the project put forward was never going to stand without the support of the fans. No-one ever thought differently in England. Over these 48 hours you were very clear that it would not stand. We heard you. I heard you," he said.
"Again, I'm sorry, and I alone am responsible for the unnecessary negativity brought forward over the past couple of days. It's something I won't forget. And shows the power the fans have today and will rightly continue to have."
As well as the 15 founding members who would always be in the league, there was also a proposal that five teams would be invited to join the league each year.
However, that idea also took a blow when several clubs -- including European champions Bayern Munich and runners-up Paris Saint-Germain -- released statements saying they were committed to the Champions League.
UEFA president Aleksander Ceferin, who had previously said the 12 clubs behind a proposed European Super League were "spitting in the face of football lovers," welcomed back those who had withdrawn from the league.
"I said [on Tuesday] that it is admirable to admit a mistake and these clubs made a big mistake," he said in a statement.
"But they are back in the fold now and I know they have a lot to offer not just to our competitions but to the whole of the European game.
"The important thing now is that we move on, rebuild the unity that the game enjoyed before this and move forward together."
Later on Wednesday, Paris Saint-Germain president Nasser Al-Khelaifi was elected chairman of the European Club Association (ECA), replacing Agnelli who quit on Sunday upon the announcement of the Super League.
The ECA represents over 200 clubs from 55 UEFA member associations and was created with the purpose of helping them safeguard their interests in European club football.
"I am honoured and humbled to have been appointed by my fellow ECA Executive Board Members as chairman," Qatari Al-Khelaifi said in a statement.
"The leadership, integrity and togetherness of our organisation has never been more required than at this pivotal moment in European football.
"I, alongside all my fellow ECA board members and clubs, am looking to reinforce ECA in its role as the legitimate and singular voice of Europe's clubs."