The move will allow for “consultations” over leaders’ future relationship with the US.
Days of protests followed Mr Trump’s announcement, leading to arrests and a number of deaths.
The UN General Assembly voted overwhelmingly to call on the US to row back its decision.
Husam Zomlot was recalled by Palestinian foreign minister Riad al-Maliki.
Mr Al-Maliki said discussions would take place “to set the decisions needed by the Palestinian leadership in the coming period regarding our relations with the US.”
Mr Zomlot is expected to return to “his normal work” after the consultation, he added.
Mr Trump’s decision upended decades of US foreign policy and countered an international consensus that the fate of Jerusalem should be determined in negotiations.