Juve finished sixth in Serie A and will compete in the Europa League next season after missing out on Champions League qualification.
Comolli said the club would have to adjust their transfer plans following a disappointing campaign but insisted he was aligned with owner John Elkann and coach Luciano Spalletti on the changes required.
"We will have to sell one more player than we had planned. Both agreed that it makes sense," the Frenchman told Italian daily la Repubblica.
"This does not mean we will weaken: every player sold will be replaced by one of equal level, if not higher."
Asked about selling highly rated youngster Yildiz, Comolli was unequivocal: "Certainly not," he said.
He conceded uncertainty remained over Vlahovic's future.
"We would like to continue, how I don't know. He told us, let's meet at the end of the season. That's it," Comolli said.
Comolli took responsibility for the club's underwhelming performances but stressed that his relationship with Spalletti remained strong, dismissing speculation of tension between the pair.
"It is false. My relationship with Luciano is constant and positive, also on a personal level," he said.
"We have been working together for just seven months, we didn't know each other before, but I am the one who recommended his name because I am convinced he is the right person. That is why I insisted on extending his contract without waiting for the end of the season."
He outlined a three-to-five-year rebuild, saying Juve were committed to a long-term project but faced pressure to deliver results sooner.
Financially, missing out on the Champions League has had a significant impact.
According to Calcio e Finanza, Juve are expected to earn around 14.6 million euros ($16.99 million) from the Europa League, compared to an estimated 42.6 million euros from Europe's top competition.
The shortfall, coupled with squad adjustments ahead of next season, means immediate success cannot be guaranteed.
"Our objective is to put the team in a position to win," he said.
"We do not know when that will be, it cannot be in five years, but I cannot say whether it will be next year or the year after, it also depends on competitors' plans."