King Hamad and Sheikh Mohamed discussed bilateral co-operation that benefits the mutual interests of their countries and furthers the progress and prosperity of their people, news agency Wam said.
King Hamad expressed his appreciation to Sheikh Mohamed for hosting the meeting of a number of Arab leaders.
On Wednesday, Sheikh Mohamed held high-level talks with leaders from across the region.
Bahrain's King Hamad and King Abdullah II of Jordan also took part.
The leaders held their discussions at the St Regis Saadiyat Island Resort.
They reviewed friendly ties between the nations and aspects of co-operation aimed at bolstering stability and prosperity in the region, Wam said.
They also discussed regional and international developments, as well as the challenges the Middle East is experiencing politically, economically and in matters of security.
The leaders spoke about the importance of co-ordinating positions and strengthening joint Arab action in dealing with these issues, to ensure a more stable future for the region.
On his visit to King Hamad's residence in Abu Dhabi, Sheikh Mohamed was accompanied by Sheikh Hamdan bin Zayed, Ruler's Representative in Al Dhafra Region; Sheikh Abdullah bin Zayed, Minister of Foreign Affairs and International Co-operation; Sheikh Hamdan bin Mohamed bin Zayed; Sheikh Mohammed bin Hamad bin Tahnoun, Adviser for Special Affairs at the Ministry of Presidential Court.
The meeting was also attended by Maj Gen Sheikh Nasser bin Hamad Al Khalifa, National Security Adviser.