In video statement posted online a group of nine Free Syrian Army commanders rejected the dismissal of General Salim Idriss as "void", accusing the opposition Interim Defence Ministry of dividing the joint Chiefs of Staff and revolutionary groups on the battlefields.
The statement said the leader of Supreme Military Council is an elected and legitimate leader.
The Free Syrian Army sacked Idriss after he fell out with the Saudi-supported head of the moderate opposition to Bashar Assad, opposition sources said on Monday.
Idriss, whose relations with Saudi Arabia deteriorated after he opened channels with Qatar, was replaced by Brig. Gen. Abdel-Ilah Bashir, head of FSA operations in Quineitra province bordering the Israeli-occupied Golan Heights, the sources said.
Idriss was visiting the United Arab Emirates when he learned of his sacking, the sources said. He still has supporters within the SMC and could try to contest the decision with their help.
Dissident rebels have long been wary of accepting Idriss, who has spent most of his time outside Syria, since being chosen as a consensus figure to lead the Supreme Military Council set up with Arab and Western backing in December 2012.