The bird flu link was found in tests using World Health Organisation equipment according to the Azeri health ministry.
The highly pathogenic H5N1 flu strain was identified in the victims on Monday, health ministry spokesman Samaya Mamedova told Russian news agency Itar-Tass.
Deputy Health Minister Abbas Velibeyov said the victims - who died earlier this month - all hailed from the Salyan region, south of the capital Baku, according to a BBC report
The tests did not confirm the presence of the virus in six other patients hospitalised with flu symptoms in the same area.
The H5N1 virus was first identified in birds early this month in Azerbaijan's Gilyazi region, near the Caspian Sea, where half a million birds have since been destroyed.
The three deaths have not yet been officially confirmed by the WHO.
If verified, they would bring the human death tally worldwide into three figures, to 101.
Most of those killed by the virus were in Asia, and died after eating or handling virus-affected birds.
A total of 22 people have died of bird flu in Indonesia, 14 in Thailand and 10 in China.
Four victims have succumbed to the disease in Turkey, another four in Cambodia and two in Iraq.
But experts fear the virus may mutate into a form that could be transmitted from person to person, touching off a global pandemic.