The crossing had been closed since August 2004, in the wake of a terror attack on the site.
More than 1,500 Palestinian workers are expected to enter Israel Thursday and another 500 workers would be allowed into the Erez industrial area
adjacent to the crossing.
Another 2,000 Palestinians have been granted access into Israel from the West Bank.
Series of IDF-Palestinians clashes
IDF soldiers and armed Palestinians continued to clash Wednesday, despite the recently declared cease-fire at the Sharm el-Sheikh summit.
An IDF source said a Hamas member was killed while trying to place an explosive devise near Khan Yunis. The source said he was killed due to a mishap and not by IDF fire.
In a separate incident, Palestinian sources in Gaza said an al-Aksa Brigade member was killed by IDF fire while attempting to fire a missile at a military vehicle.
In southern Gaza IDF troops fired warning shots after identifying four Palestinians approaching a Jewish settlement. One Palestinian was injured.
In the West Bank, Palestinians threw stones at security fence construction workers northeast of Ramallah. One person was lightly injured and damage was caused to his car.