The Erez crossing for people and the Kerem Shalom crossing for goods reopened Sunday morning, a spokeswoman for COGAT, the defence ministry unit that oversees the crossings, told AFP.
Closed on Monday, the reopening comes after tens of thousands of Palestinians protested along the Gaza border with Israel on Saturday, to mark the one-year anniversary since demonstrations and clashes erupted there.
Four Palestinians were killed on Saturday during protests and clashes, but unrest was limited and fears of mass bloodshed were averted after Egyptian-led negotiations.
Five rockets were launched from the Gaza Strip at Israel overnight, leading Israeli tanks to fire on Hamas military posts. No casualties were reported from either the rockets or tank fire.
Hamas officials say an understanding was reached that would see Israel ease its crippling blockade of Gaza in exchange for the protests remaining calm.
Israel, which has fought three wars with Hamas since 2008, has not commented on the claims of an agreement.
Israel goes to the polls in a keenly contested general election on April 9 in which Prime Minister Benjamin Netanyahu faces a stiff challenge from centrist former military chief Benny Gantz.
In public remarks on Thursday, he said Israel would only undertake a broad military campaign in Gaza after exhausting all other options.