The woman approached the crossing point in Qalandia, between Jerusalem and the occupied West Bank, in a lane designated for vehicles despite repeated calls from guards to stop, a statement said.
She was wounded when security forces opened fire, police spokesman Micky Rosenfeld said, adding that her injuries were not thought to be life-threatening.
Police said she was 35 and from Issawiya, a neighbourhood in east Jerusalem.
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She was left for around an hour after the attack on the ground before receiving treatment, an AFP photographer at the checkpoint said.
Israel public radio said forces checked her for explosives before allowing her to be transported to a nearby hospital.
Since October 2015, 246 Palestinians, 36 Israelis, two Americans, a Jordanian, an Eritrean and a Sudanese have been killed in a wave of violence, according to an AFP count.
Most of the Palestinians killed were carrying out knife, gun or car-ramming attacks, according to Israeli authorities.
Others were shot dead during protests or clashes, while some died in Israeli air strikes on the Gaza Strip.