The summit in Equatorial Guinea said the warrant issued last week "seriously complicates" efforts to find a peaceful solution to the conflict between Gaddafi's forces and Libyan rebels.
An assembly of the summit decided that "AU member states shall not cooperate in the execution of the arrest warrant," according to a text of the decisions.
The warrant "seriously complicates the efforts aimed at finding a negotiated political settlement to the crisis in Libya, which will also address, in a mutually reinforcing way, issues related to impunity and reconciliation," it said.
The 53-nation African Union took a similar stance against an ICC warrant for Sudanese President Omar al-Bashir in 2009 on charges of genocide, war crimes and crimes against humanity in Darfur.
The ICC on June 27 issued warrants for Gaddafi, his son Seif al-Islam, and the head of Libyan intelligence, Abdullah al-Senussi, for atrocities committed in a bloody uprising that began mid-February.
The summit that opened outside the capital Malabo yesterday also agreed on a roadmap out of the Libyan conflict, in which five African leaders are mediating.