The 69-year-old quit almost exactly one year after selling a 70 percent stake in the club to a consortium led by Indonesian business tycoon Erick Thohir, who replaced Moratti as club president.
"Massimo Moratti has today resigned as honorary president of FC Internazionale Milano Spa, a position kindly offered to him by Mr Erick Thohir in November last year," said a statement issued by Internazionale Holding Srl, a holding company owned by Moratti and his two sons.
No reason was given for the decision.
Inter won five Serie A titles in successive years during Moratti's 18-year reign, between 2006 and 2010, and also clinched the Champions League and UEFA Cup once each and the Coppa Italia four times.
The highlight was the Champions League, Serie A and Coppa Italia treble under Jose Mourinho in 2010.
Moratti, whose father Angelo owned the club from 1955 to 1968, brought a host of big signings to Inter, including Brazilian Ronaldo, Hernan Crespo, Adriano, Roberto Baggio, Zlatan Ibrahimovic, Luis Figo, Patrick Vieira and Samuel Eto'o.
However, he had little patience with coaches, employing 18 during his presidency including the hapless Gian Pieri Gasparini, who was fired after only five matches in 2011.
Inter finished fifth last season and have made an inconsistent start to the new campaign, currently in ninth place.
(Writing by Brian Homewood in Berne, Editing by Neville Dalton)
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