The 22-year-old was one of four New York-based students who launched Diaspora as a “privacy-aware, user-controlled” social network.
It was set up in response to criticism that Facebook was not handling the privacy of its users well.
The cause of Mr Zhitomirskiy’s death is yet to be determined. The San Francisco coroner’s office said it will have details in several weeks time.
In tribute, the home page of Diaspora featured a giant dandelion seed head next to an image of Mr Zhitomirskiy.
Public memorial services are being planned for Mr Zhitomirskiy in San Francisco later this week.
A statement by co-founder Peter Shurman said: “We’ll all miss Ilya more than we can say. Ilya was a great friend and a brilliant person, a visionary whose work for a better future online brought hope to many people.”
The site was launched a year ago by Mr Zhitomirskiy and three fellow students at New York University. Facebook’s co-founder, Mark Zuckerberg, said he donated an undisclosed sum to the project.
Diaspora featured pages that were similar to those on Facebook but offered simpler privacy settings. However, its launch was not without criticism.
When it released its first code in September, developers found multiple security bugs. Some also questioned whether the team could deliver their vision.
It is one of several sites – including Appleseed, OneSocialWeb and Elgg – that aims to challenge Facebook’s model.