The Portuguese star scored both goals in Friday's 2-1 win over Lyon, but the Italian champions were eliminated on the away goals rule, having lost the opening leg of their last-16 tie in France.
With the defeat, Ronaldo missed out on the quarterfinals of the Champions League for the first time since 2010, when he was with Real Madrid.
There have been rumblings in the wake of Friday's result that the 35-year-old could leave the club, with Paris Saint-Germain tipped as a potential suitor.
But, Agnelli moved quickly to pour cold water on that suggestion.
"I am entirely convinced he will stay," Agnelli said after Friday's match, according to ESPN. "I think the report was down to an interview from several months ago, which just happened to be published just before we played against a French team.
"It's an old media trick. No, I can assure you that Ronaldo remains a pillar of Juventus."
Juventus announced on Saturday that manager Maurizio Sarri was fired, meaning Ronaldo will work with his third coach in three seasons if he remains in Turin next year.