Officials complained the outlets - including two of Somalia's largest independent broadcasters and the local office of the Al Jazeera Channel (Arabic) - aired unconfirmed reports and leaned towards the Union of Islamic Courts fighters routed by an Ethiopian-led offensive.
But Monday's closures brought the government unwelcome publicity and protests from both local and foreign media watchdogs, which said it was an affront to democracy.
Media executives emerged from a lengthy meeting with government officials on Tuesday to announce they were going back on the air.
Ali Iman Sharmarke, co-owner of HornAfrik broadcaster, told Reuters: "The government reversed the ban. The international media and international organisations, especially the ones who work to protect the media, played a major role in the lifting of this ban."
The 24-hour closure of the outlets came as martial law was declared across Somalia weeks after an Ethiopian-led military offensive ousted Union of Islamic Courts fighters in the south.
Gabriel Baglo, Africa office director of the International Federation of Journalists, said: "Shutting down private media houses is the worst way to reconcile the Somali people and to bring the country out of these long periods of chaos."
Al Jazeera English's correspondent in Mogadishu, Mohammed Adow, confirmed that the radio stations of HornAfrik and another major independent broadcaster, Shabelle Media Network, could be heard soon after the media executives met government security officials.
Ethiopia wants to pull out its soldiers in the coming weeks. But diplomats fear that would leave a security vacuum around the weak fledgling government, which has called for the urgent deployment of a promised African Union (AU) peacekeeping force.
As president of the east African regional body IGAD, Mwai Kibaki, Kenya's president, is leading a regional push to muster an African mission. Kibaki discussed the issue with Meles Zenawi, the Ethiopian prime minister, during a surprise visit to Nairobi.
In a joint statement, the two leaders called on Tuesday for "immediate deployment" of an AU-IGAD peacekeeping force.
"The two leaders welcomed the offers made by a number of African countries to contribute troops and invited other African countries to support the initiative."
Only Uganda has publicly offered to contribute, and analysts are sceptical as to whether a mission can even be put together let alone come to grips with Somalia's myriad problems.
The latest attack on an Ethiopian convoy in northern Mogadishu underlines the challenge Yusuf and Gedi face taming a country in anarchy since the 1991 ousting of Mohamed Siad Barre, the president.
A doctor said eight people were wounded while a government source said three Somalis died in the assault late on Sunday.