Jamal al Jamal died at a hospital in Prague where he had undergone surgery, the New York Times reported.
Police said the blast did not appear to be the work of terrorists.
"We do not have a single indication that this could be a terrorist attack," Police President Martin Cervicek said.
Jamal became ambassador Oct. 11. He and his family had just moved into a new residence, and the Palestinian Ministry of Foreign Affairs said the safe had been moved from the old embassy.
Czech Radio reported the ambassador's family was in the residence when the bomb detonated about noon.
The residential neighborhood where many diplomats live in Prague was barricaded while explosives experts with dogs searched Jamal's residence and the area, Radio Prague said.