The two commanders were named as Mohsen Saleh Hadi Gawd and Salah Jorman.
Zaidi fighters, who are also referred to as Houthis after their leader Abdul-Malik al-Houthi, have been fighting a campaign for independence in the north for the past five years.
Sana'a launched Operation Scorched Earth against the Houthis two weeks ago in an attempt to end the insurgency.
Fighting began in the northern Saada province, which borders Saudi Arabia, and spread to Amran province.
President Ali Abdullah Saleh on Friday reaffirmed six conditions for a ceasefire, which includes withdrawal from the mountainous region and return of military hardware.
He warned that the full capabilities of the government would be used against Houthis if a ceasefire was not agreed.
Abdul-Malik al-Houthi rejected the terms, saying the government was seeking to "mislead the public opinion".
The Houthis or Zaidi, an offshoot of Shia Islam, are the majority group in the north of Yemen but a minority nationwide and aim to re-establish the autonomous rule they held before a coup in 1962.
Thousands of people have been killed since the conflict began in 2004.
More than 35,000 people have been displaced, the UN has said.