Jota and brother Andre Silva, who also played for Porto, were laid to rest on the weekend after losing their lives in a fatal car accident in Spain last week.
Speaking at the funeral, Villas-Boas said: "Unfortunately, we were working with agent Jorge Mendes on Diogo Jota's return to FC Porto, and it won't be possible.
"It would be from 2026-27, and we had discussed the possibility. I made a point of conveying that message to Diogo, through Jorge Mendes, at his wedding, and it was a dream for all the Porto fans that it would happen."
AVB also said: "Diogo has a history in the senior ranks, and André has many years from the children's ranks to the under-19s. They were much loved. We've come to pay our respects to the family.
"Diogo, especially as the greatest public figure, was a silent hero. We all appreciated him for everything he stood for, not only on the pitch but also off it.
"He was a partner of FC Porto with its Esports team. Someone who will be remembered fondly, just like his brother."
Now FC Porto members
"Diogo wasn't a member (of the club), but he became one today," Villas-Boas added. "I hope that all FC Porto members understand this move.
"In André Silva's case, we symbolically recovered his membership fees and gave them to his family. We intended to leave the two membership cards here. I did it as chairman of the board.
"Condolences to everyone, to the team-mates from Liverpool, Wolverhampton, Gondomar and P. Ferrreira. And Penafiel, who also lost a great mate. It's tragic and deserves a moment of reflection."