He escaped only to be captured by Chadian rebels who control a patch of territory close to the Libyan border.
Libya said its troops were not involved in the fighting, which it said was between two groups of Chadian rebels.
Sudan's official news agency stated that Chadian rebels had driven off government reinforcements moving toward the city from southern Chad.
The Chadian rebels operate from a base that journalists have visited in Sudan.
Chadian rebels said that they would attempt to block the May 3 election.
Zouar was reportedly taken by the Libyans six days ago from Chadian rebels who were once their allies.
In March, Chadian rebels captured 17 members of the group after a battle near the border with Niger.
The Chadian rebels don't have the proper means to launch an offensive, the Sudanese can easily control them.
From this position the troops assisted Chadian rebels in carrying out raids against government forces in Chad.
That Chadian rebels have found sanctuary in Sudan is beyond doubt.