The move by Pope Tawadros II came after Palestinian leaders also said Mike Pence, who's scheduled to visit the region this month, was no longer welcome in the territories.
In a statement, the Coptic Orthodox Church of Egypt said it "excused itself from hosting" Mr Pence when he visits the Egyptian capital of Cairo on 20th December.
Pope Tawadros II
It added that President Donald Trump's decision "did not take into account the feelings of millions of Arab people".
Tensions have risen since Mr Trump announced that the US embassy in Israel would be moved from Tel Aviv to Jerusalem.
Hamas has claimed two people have been killed after Israeli warplanes struck military targets in Gaza.
Israel have said the attacks were in response to three Palestinian rocket attacks.
The Arab League says Donald Trump's decision to recognise Jerusalem as the capital of Israel is a "dangerous violation of international law".
Foreign ministers from the organisation's member states are urging the US to abandon the move.
They also say they'll seek a United Nations Security Council resolution to reject it.
Meanwhile, about 10,000 people have rallied outside a US Embassy in Indonesia to support Palestinians and denounce the decision to recognise Jerusalem as Israel's capital.
The protesters in Jakarta carried banners reading "US Embassy, Gets Out from Al Quds", ''Free Jerusalem and Palestinians" and "We are with the Palestinians".
Al Quds is the Arabic name for Jerusalem.
The protest on Sunday, organised by the Islamist Prosperous Justice Party, was the second since US president Donald Trump's decision on Thursday.
