She called on them "to suspend the operations of Kadhafi's embassies in your countries, to expel pro-Kadhafi diplomats" and to increase support for and contact with the National Transitional Council (NTC).
"Your words and your actions could make the difference in bringing this situation to a close and allowing the people of Libya ... to get to work writing a constitution and rebuilding their country," she said.
Senegal and Gambia are the only African states to have recognised the NTC as the legitimate interlocutor of the Libyan people, something the United States, Britain, Australia, France, Italy, Qatar and the United Arab Emirates have done.
On the third and last leg of an Africa tour that has taken her to Zambia and Tanzania, Clinton said the world needs the African Union to lead.
She said the AU can help guide Libya through a transition to a new government based on democracy, economic opportunity and security, a transition she said they describe in their own statements.
The lights in the conference room went out ten minutes or so into her speech but Clinton appeared unfazed and carried on in the dark saying: "when things like this happen, you just keep on going."
US diplomats have praised countries like South Africa, Nigeria and Gabon for supporting UN resolutions that opened the way for NATO-led military action against Kadhafi's regime.
But they said many countries have been reluctant to take a tougher stand as Kadhafi's oil money has provided them with key financial support. African institutions, including the AU, have also benefited, they said.
Clinton's comments drew harsh criticism from Democratic Representative Dennis Kucinich, a fierce critic of US involvement in the Libyan conflict who charged in a statement that she was "threatening" Africa.
"Africa is not an imperial holding of the United States," he scolded. "Africa should be left to make its own decisions about its dealings with Libya without undue pressure from the United States."
Clinton praised the more than half of the 53 countries in Africa that have embraced democratic, constitutional and multi-party rule, but she asked the remaining autocracies to heed the warnings from the "Arab Spring" revolutions.
"Rise to this occasion, show leadership by embracing a path that honous your people's aspirations," she said.
"Create a future that young people will believe in, defend and help build."
If they fail to do so, she warned, "you will be on the wrong side of history and time will prove that."
Clinton also praised Africans for increasingly taking on the responsibilities of solving Africa's own problems and crises, alluding to examples like the deployment of African peacekeeping forces in Somalia.
She referred to the role of the African Union and subregional organizations, which include SADC in southern Africa and ECOWAS in west Africa.
Instead of providing temporary aid, Clinton said, the United States is now taking a different approach to promoting development in Africa by helping its economies grow to the point they can meet their own needs.
At the start of her tour in Zambia, Clinton urged African nations to remove trade barriers not only within Africa but with the United States, which offers tariff-free trade to most African countries.
Clinton reiterated those points to the AU, about the need to trade not only internationally but within Africa.