The protesters also set fire to an annex of Shafiq's office, hours after election commission announced that the second round of the historic polls is to be held between Muslim Brotherhood candidate Muhamamd Mursi and Shafiq, a former Prime Minister and also a former Air Force commander.
A secretary working at the Shafiq's campaign offices told Egypt Independent that the campaign workers were notified to leave before the fire started.
The fire was later extinguished without causing any casualties. Some suspects have been arrested, police said. Shafiq's supporters later gathered outside the headquarters, chanting, "Down with the Supreme Guide (of the Muslim Brotherhood)," and "The poll will show Shafiq is the President", the paper said.
Last week's voting was Egypt's first freely contested presidential election, which saw a turnout of 46%.
Two of the defeated candidates earlier demanded a recount, citing violations, a claim rejected by the High Commission for Presidential Elections.
Commission head Farouq Sultan yesterday said that Mursi and Shafiq finished as the top two candidates, with each receiving more than five million votes.