The Council adopted a resolution that hands over responsibility for maintaining security to Sudan's transitional government.
Saudi Arabia's religious affairs minister said the move highlighted the importance of following state directives.
Indonesian Muslim groups and pro-Palestine NGOs have slammed the prospect of normalising ties with Israel.
President Donald Trump's special advisor and son-in-law has spearheaded normalisation agreements between Israel and Arab states this year.
A normalisation agreement between Israel and Morocco was signed in the presence of the king as well as an Israeli delegation headed by Donald Trump's son-in-law, Jared Kushner.
Analysis: Fearing a reversal of policies under the Biden administration, Israel and the UAE are exploiting the last days of Trump's presidency to shore up a new geopolitical reality.
US President Donald Trump's son-in-law Jared Kushner landed in Rabat on Tuesday on the first first direct commercial flight between Israel and Morocco.
The move follows similar actions by Saudi Arabia and the UAE's fatwa councils.
Talks to demarcate the border between Sudan and Ethiopia started talks on Tuesday, just a week after deadly clashes in the disputed area.
Sudan was granted legal immunity for past militant attacks on Monday, a final step in a historic deal removing it from Washington's blacklist of state sponsors of terrorism.