The suspects, named as Omar Asim and Abuliezi Abuduhamiti, were arrested on charges of being members of a terrorist organization, of purchasing unlicensed firearms and being accomplices to the murder of 39 people.
A witness in the central Anatolian city of Konya had reportedly seen Asim with the Reina nightclub attacker.
The gunman remains at large despite a massive manhunt, the New Arab reported.
Officials said last week the attacker was likely a Turkic Uighur, with authorities reportedly looking into the possible existence of a cell, including other extremists from Central Asia.
Uighurs are Turkic-speaking groups from the restive Xinjiang region of far-western China.
The killer, reportedly known by the code name Ebu Muhammed Horasani, slipped into the night after killing 39 revelers at the Reina nightclub just 75 minutes into 2017.
At least 35 people have been detained so far in connection with the attack.
Of the 39 killed in the glamourous nightclub on the shores of the Bosphorus, 27 were foreigners including citizens from Lebanon, Saudi Arabia, Israel, Iraq and Morocco.