The two suspects, who weren't identified, were detained in the city of Sanliurfa, near the border with Syria, on Saturday, the Anadolu Agency reported.
A court in Istanbul charged them with premeditated murder and membership in a terror group today, it said.
Ten Syrians were charged with membership in a terror group and ordered jailed pending trial on Sunday.
The suicide bomber set off the explosion near a group of German tourists on Jan. 12, just steps away from the landmark Blue Mosque, killing ten of them. Fifteen other people were wounded in the blast.
The bomber has been identified as Nabil Fadli, a Syrian national born in 1988 who had registered as a refugee with a migration agency in Istanbul a week before the attack.
Officials haven't disclosed any information on the suspects or say what links they have to the bomber.
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