Falk flew into Tel Aviv on Sunday night and spent the night at Ben Gurion airport before he was deported this morning.
Earlier this year, when the Princeton University professor of international law was appointed as the UN's special rapporteur in the Palestinian territories, Israel said it would deny him entry because in 2007 he said the Jewish nation's blockade on the Palestinian coastal territory of Gaza was a "Holocaust in the making".
In June this year, Israel allowed Falk to enter in a personal capacity to attend a conference in Ramallah in the occupied West Bank.
Israel defended its decision to deport Falk, saying he had used his personal visit in June to write an official UN report and because of his "shameful comparisons to the Holocaust".
Israel also objects to the UN's special rapporteur mandate which aims to document only the Jewish state's abuses of Palestinian human rights. It does not include Palestinian abuses of Israeli human rights.
It's the third time this year that Israel has barred a high-profile critic from entering.
In May, it deported Norman Finkelstein, a controversial Jewish American academic who has accused Israel of using the Holocaust to justify its actions against the Palestinians. Israel also refused Nobel peace laureate the Archbishop Desmond Tutu entry while on a UN fact-finding mission in Gaza the same month.