The suspects, named as Omar Asim and Abuliezi Abuduhamiti, were arrested on charges of "being members of a terrorist organisation", of "purchasing unlicensed firearms" and "being accomplices to the murder of 39 people", state-run Anadolu Agency cited a prosecutor as saying.
A witness in the central Anatolian city of Konya had reportedly seen Asim with the Reina nightclub attacker, the agency said late Friday.
The gunman remains at large despite a massive manhunt.
Officials said last week the attacker was likely a Turkic Uighur, with authorities reportedly looking into the possible existence of a cell, including other jihadists from Central Asia.
Uighurs are Turkic-speaking Muslims 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 mowing down 39 revellers at the Reina nightclub just 75 minutes into 2017.
At least 35 people have been detained so far in connection with the attack, according to Anadolu.
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.
The so-called Islamic State claimed the nightclub massacre, the first time it has ever clearly claimed a major attack in Turkey despite being blamed for several strikes including the Istanbul airport bombings.
