A Reuters witness saw buses provided by the army transporting around 100 Palestinians from Erez crossing southward to the Israeli-Egyptian border. An Israeli military spokeswoman said the passengers would cross into Egypt under a deal struck with Cairo.
The IDF also reported that the defense establishment examined each particular case individually and the evacuation was only carried out after meticulous security checks and under tight security.
The Palestinians were among some 120 people linked to the Fatah faction who fled possible reprisals after the secular Fatah was routed by Hamas Islamists in Gaza fighting last week.
After holing up at Erez, one of the Palestinians was killed and several wounded during a shootout between a Palestinian gunman and Israeli troops stationed on the border.
Israel at first balked at the Palestinians' request to leave Gaza through its territory, citing fears that there could be militants among them.
But the policy was loosened on Wednesday after Israeli Defence Minister Ehud Barak gave orders to bring out the casualties for treatment in the Jewish state.
Ynet contributed to this report