The United States on Wednesday had demanded that the report be withdrawn altogether.
A statement said Abbas "stressed to Dr. Khalaf that our people appreciate her humanitarian and national position".
Khalaf stood by the report, calling it the "first of its kind" from a United Nations agency that sheds light on "the crimes that Israel continues to commit against the Palestinian people, which amount to war crimes against humanity".
The U.N.is "incapable of taking a stand" and the debacle over the report proved it can not be counted on "to defend human rights in our region", he said.
Palestinian Authority President Mahmoud Abbas addresses a graduation ceremony for public sector employees in Ramallah on March 12, 2017.
Khalaf, under-secretary general and executive secretary at the UN Economic and Social Commission for Western Asia (ESCWA), told a news conference: "The secretary general asked me yesterday morning to withdraw (the report)".
"We in Jordan view worldwide reports about what the Palestinian people are being subjected to, from daily restrictions to injustice, as something that is in their interest", he said.
Meanwhile, Israel's United Nations envoy Danny Danon and Washington's ambassador to the world body, Nikki Haley, welcomed Khalaf's resignation.
Danon said Guterres's move was "an important step in stopping discrimination against Israel".
Israeli envoy to the UN, Danny Danon, too said it was "long overdue".
On the same day of the report's release, Khalaf said the "ignorance of the global community" in recent decades had "encouraged Israel to continue its abuses of worldwide law".
Palestinian Minister of Foreign Affairs Riyad al-Maliki also voiced deep regrets that Khalaf was forced to resign and expressed his "unequivocal objection" over the removal of the report.
"U.N. agencies must do a better job of eliminating false and biased work, and I applaud the Secretary-General's decision to distance his good office from it", Haley said in a statement.
Palestinian President Mahmoud Abbas has awarded the highest Palestinian honour to Rima Khalaf, a senior United Nations official who resigned on Friday amid pressure to withdraw a report that accused Israel of creating an apartheid state.
A Palestinian rights activist, Omar Barghouti, described the report as potentially the "first beam of light that ushers the dawn of sanctions against" Israel.
As of shortly after noon Friday, a previous link to the report yielded an error message and the report was not listed among the publications on the website for the ESCWA, an agency based in Beirut, Lebanon that is comprised of 18 Arab member states, including what is identified as the State of Palestine.