Mr Marzouki was swiftly evacuated by security officers, disrupting his rally to mark the anniversary.
A vendor set himself alight in Sidi Bouzid in December 2010, starting the uprising that ousted the former regime.
But the new government has faced a series of protests, as people accuse it of failing to improve their lives.
Protesters invaded the square where Mr Marzouki had addressed a crowd of about 5,000 people, AFP news agency reports.
They threw tomatoes and stones, forcing security officers to evacuate him and parliamentary Speaker Mustapha Ben Jaafar.
The protesters shouted “the people want the fall of the government” – one of the rallying cries of the revolution that overthrew long-serving ruler Zine al-Abidine Ben Ali in January 2011.
In his speech, Mr Marzouki promised economic progress within six months to the residents of Sidi Bouzid, a poor town in central west Tunisia, AFP reports.
Source: BBC
Tomato protest for Tunisia leader
Protesters have thrown tomatoes and stones at Tunisia’s President Moncef Marzouki in Sidi Bouzid, where the Arab Spring started exactly two years ago.
