The Hamas-controlled Gaza Strip has been of particular concern for the spread of the coronavirus due to its high population density.
The border with the Palestinian territory is mostly shut but opens at regular intervals. This would be the longest single opening in years.
Egypt last opened the crossing more than two weeks ago.
The Palestinian Embassy in the Egyptian capital did not say why the crossing was closed early.
Pictures shared on Twitter on Wednesday show dozens of Palestinian standing in crowded spaces in the passageway.
Egypt had planned to open the crossing for 3 days, but unexpectedly closed it early, leaving Palestinians stranded.
Egypt tends to open the frontier temporarily a few times a year, usually with short notice and little explanation.
Egypt was slated to open the crossing from Saturday until Monday in both directions
The failure to open the crossing came approximately a month after Egypt brokered a deal between Hamas and Fatah to advance reconciliation efforts and restore the PA’s governing authority in Gaza.