The 40-year-old ended his playing career last month after 19 seasons with Inter.
Zanetti made 857 appearances for the San Siro outfit and won 16 trophies since moving to Inter from Banfield in 1995.
"The (club's administration) council has decided to withdraw the number four jersey," Thohir said to Gazzetta dello Sport.
Thohir, who took over ownership of Inter last October, also confirmed that Zanetti will continue at the club with the former defender having accepted the role of vice-president.
"Zanetti will be vice-president of Inter Milan for the next two years," Thohir said.
Inter have also offered coach Walter Mazzarri a one-year contract extension which will keep him in charge of the Nerazzurri outfit until June 2016.
Mazzarri was appointed as head coach last summer, replacing Andrea Stramaccioni, who had overseen a poor 2012-13 campaign in which Inter finished ninth in Serie A.
The 52-year-old Mazzarri led Inter to a fifth-placed finish in his debut season in charge.
"We hope to be able to announce soon Mazzarri's renewal," Thohir said.
Mazzarri will have Mauro Icardi in his roster next season with Inter having turned down a lucrative offer to sell the Italian forward, according to Thohir.
Reports in Spain claim Atletico Madrid have made a 31million euros offer to acquire Icardi and Inter goalkeeper Samir Handanovic.
"We have received an offer but we don't want to sell Icardi," Thohir said. "It's important for us to have a strong team."
The 21-year-old Icardi scored nine goals and set up two more in 22 league appearances for Inter in the 2013-14 campaign.
Inter will compete in the Europa League next season.