Fox was due to make his last ever speech to the country's parliament when dozens of opposition politicians stormed onto his podium on Friday afternoon.
Some of the members of parliament held up banners which read 'Fox is a traitor to democracy' shortly before he was to appear on national television.
The parliament's speaker ordered a recess after the opposition MPs refused to return to their seats.
The outgoing Mexican president then handed a written version of his speech to congress officials and said he was leaving without trying to deliver the address.
The leader of the opposition, Andres Manuel Lopez Obrador, alleges that Fox fraudulently helped fellow conservative Felipe Calderon, the former energy minister, to win the country's July election.
Lopez Obrador has vowed to make Mexico ungovernable until a full recount of votes is held,
Supporters of Lopez Obrador gathered in Mexico City's central Zocalo square on Friday to protest what Lopez says are "corrupt institutions such as the courts".
Speaking to the crowd, Lopez said: "To hell with their institutions."
But he also urged the crowd to be peaceful and not march on congress a few miles away.
"Our movement will always be peaceful. We will not fall into any trap or allow ourselves to be provoked," Lopez said.
Some followers were disappointed by the call to stay away from the legislature.
Joel Mendoza, 49, from Acapulco said: "We need a bit of action, no? Some of us would liked to have gone."
Police deployed 6,000 officers equipped with water cannons and used meta; barricades to block streets and subway stations near the parliament but were not able to stop protesters from massing a few blocks away.
Since the crisis erupted, Fox's approval rating have hit 68 per cent, its highest level since 2001, in a poll in the Reforma newspaper on Friday. Another poll in El Universal showed him with a 67 percent rating.
Felipe Calderon, who won the vote by 244,000 votes out of 41 million, is expected to be named president-elect in coming days after the court rejected Lopez Obrador's fraud claims and refused the full recount he demanded.