President Pranab Mukherjee inaugurated India- Palestine Centre For Excellence at the Al-Quds University in Abu Dis on Tuesday.
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He later paid homage to Theodor Herzl, founder of modern political Zionism, at his cemetery in Israel, apart from visiting memorials and educational facilities on the west side of Jerusalem.
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This is the first visit by an Indian head of state to Israel and Palestine in three decades. President Mukherjee's visit comes at a time when tensions between Palestine and Israel have risen, causing heavy casualties.
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President Mukherjee visited the Palestine city of Ramallah on Monday before returning to Israel capital Tel Aviv on Tuesday for a three-day visit.
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He is on a six-day visit to Jordan, Palestine and Israel.