Details of the discussion and the meeting between the visiting top Iranian commander and the Turkish president have not been already released.
In a meeting with Turkish Defense Minister Nurettin Canikli on Wednesday, Baqeri stressed respecting sovereign states' territorial integrity.
He added that adopting the policy of non-interference guarantees security, peace and stability of the region.
Baqeri arrived in Ankara on Tuesday for an official three-day visit and met with his Turkish counterpart General Hulusi Akar.
Major General Baqeri and the accompanying delegation are in Turkey at invitation of chief of the General Staff of Turkish Armed Forces.