The protesters threw the tomatoes, shoes and a water bottle as the staff walked to their vans after the ceremony and riot police had to hold back the crowd.
A tomato hit an Egyptian official in the face. Clinton's van was around the corner from the protesters, and a senior State Department official said her car was not hit, CNN reported.
The chants of "Monica" refer to Monica Lewinsky, the White House intern who had an affair with Clinton's husband, former president Bill Clinton.
The assault on her motorcade came on a day Clinton spoke at the newly re-opened US consulate in Alexandria, addressing accusations on the United States, which had long supported former President Hosni Mubarak, of backing one faction or another in Egypt following his ouster last year.
Clinton said she was in the city to answer critics who believe Washington has taken sides in Egyptian politics.
There were already vocal protesters at the start of her visit to the consulate, forcing the ceremony to be moved inside.
"I want to be clear that the United States is not in the business, in Egypt, of choosing winners and losers, even if we could, which, of course, we cannot," Clinton said at the ceremony to reopen the consulate, which was closed in 1993 because of budget constraints.
Earlier yesterday, Clinton held a closed-door meeting with the head of Egypt's military leadership, Field Marshal Mohamed Hussein Tantawi, whose military council is in a political tug of war with new President Mohamed Morsy.