He starred in the number 10 for Napoli and Argentina during his playing career, and the shirt was retired by the Serie A club in his honor in 2000.
Villas-Boas wants to see FIFA go one step further and withdraw the number 10 completely.
"For Maradona, it's a hard blow. I would like FIFA to withdraw the number 10 for all competitions, all teams," he told a news conference after Marseille's 2-0 Champions League loss to Porto on Wednesday.
"I think it's the best tribute that can be given to the greatest player in the history of football. It is an incredible loss for the world of football."
Villas-Boas said he would always remember his one meeting with Maradona.
"Yes, I met him once. He was a guest at the Pinetina, the Inter Milan sports centre, when I was there," he said.
"And I remember this photo, next to my trophies in Porto. Because of that, I bought a watch when Hublot had them signed by Maradona. And this watch came with a jersey signed by him that I still keep. These are good memories.
"But Maradona wasn't just that. It's his genius from the world of football, the images he leaves us, the image of his warm-up in Naples, those kinds of things that are extraordinary.
"It's a loss for everyone. I only met him once, next to each other, it's a moment I won't forget."
Maradona, the captain and inspiration behind Argentina's World Cup success in 1986 before going on to coach his country at the 2010 showpiece, had been hospitalized just days after turning 60.
He appeared in a fragile state when he briefly made an appearance as his Gimnasia y Esgrima La Plata side played a match on the evening of his birthday last month.
Maradona won 91 caps for Argentina between 1977 and 1994, scoring 34 goals at international level.
He started his career with Argentinos Juniors before joining Boca Juniors and went on to play for Barcelona, Napoli, Sevilla and Newell's Old Boys before returning to Boca in 1995.
Maradona had the best years of his club career in Italy, playing a massive part in Napoli winning the Serie A title in the 1986-87 and 1989-90 seasons.
Playmaker Maradona also lifted the UEFA Cup with Napoli in 1989 and he won three trophies during his time at Barca – including the Copa del Rey in 1983.
Maradona also had stints in charge of Textil Mandiyu, Racing Club, Al-Wasl, Fujairah and Dorados de Sinaloa in Mexico before being appointed by Gimnasia last year.