"Vagabov was the organiser of the suicide bombings on the Moscow metro, was actively involved in recruiting youth for the underground and organised the training for the suicide bombers," the national anti-terror committee said in a statement.
Chechen 'number two'
The committee described Vagabov as the number two figure in the Chechen uprising against Russia.
Saturday's clash took place in the southwest village of Gunib where the fighters were holed up in a house in the mountains. During the course of the battle, the house apparently caught fire.
"Once the fire from the building was put out, one of the corpses was identified as Magomedali Vagabov," the statement said.
Vagabov was reportedly married to Mariam Sharipova, one of the two metro bombers.
In addition to the Moscow metro attacks, he had also allegedly planned a string of attacks against security forces and on the railway infrastructure, the statement said.
Russian security forces had targeted Vagabov in previous special operations but failed to track him down until now.
'Emir of Grozny'
Russia fought two wars against separatist fighters in Chechnya in the 1990s. Now the anti-government campaign has spread to neighbouring regions of Ingushetia and Dagestan.
In a separate incident on Saturday, Khamzat Chemilev, another separatist leader in Chechnya, died while battling Russian security forces, officials said.
Chemilev, who is also known as the "emir of Grozny", was accused of carrying out attacks on markets in Moscow in 2009 and 2010.
Authorities said he was trapped in his house and told to surrender, but reacted by firing an automatic weapon and throwing hand grenades at troops before blowing himself up.