Nazmi Muhanna, the Palestinian Authority's top official for border crossings, formally received control of the Rafah crossing with Egypt from his Hamas counterpart.
At a separate checkpoint with Israel, an AFP photographer also saw Hamas installations being dismantled.
At the Rafah crossing, Palestinian and Egyptian flags were flying, with large pictures of Palestinian Authority president Mahmud Abbas and Egyptian leader Abdel Fattah al- Sisi.
Hisham Adwan, director of information at the Hamas crossings authority, told AFP that Palestinian Authority employees would resume full control of the border.
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The checkpoints had been due to be handed over by November 1 and were seen as a first key test of the strength of the reconciliation agreement.
Hamas has ruled Gaza since 2007 when the Islamists seized control in a near civil war with Abbas's Fatah, based in the occupied West Bank.
A number of issues, including the future of Hamas' vast military wing, remain uncertain.
Multiple previous reconciliation agreements have collapsed.