Authorities here have reported no fatalities from the storm, and there have been no reports of people being injured by the tempest, which struck this Caribbean island early Monday.
Coastal communities west of the capital also joined the cleanup effort Tuesday after massive waves, rains and winds ravaged the region.
"More than 2,000 homes were flooded and another 2,000 were damaged in Santa Fe, a west Havana neighborhood that was inundated," said Colonel Luis Angel Macareno, the deputy chief of civil defense.
Although parts of Havana remained flooded Tuesday, after seawater whipped up by Wilma broached the coastal city's defences, the subsiding of the waters enabled some residents to start cleaning up.
In the city's Miramar neighborhood, one of the worst-affected districts, buildings suffered substantial damage from nature's onslaught.
Authorities said at least 90,000 people had been evacuated amid flooding and storm damage in Havana, as many of the city's buildings are old and poorly maintained.
In some city streets, the floodwaters had risen to waist height, as Wilma passed en route to Florida and the Atlantic.
Rescue workers in inflatable boats patrolled some districts seeking to help those in need.
The city's electrical grid suffered serious damage during the storm, and wide areas of the capital have been without power since Wilma struck.
Authorities said some 260,000 people had been evacuated from the province of Pinar del Rio, west of the capital, after it was hit with strong rains and flooding.