An unnamed eyewitness told news agency AFP that Palestinians were hurt by stone-throwing settlers who also "shot at the Palestinians but did not wound anyone".
An Israeli army spokesman said: "Two settlers were wounded, and the army, border guards and police were trying to separate the two sides."
David Wilder, a settler spokesman, said violence flared up after a Jewish teenager was attacked by Palestinians earlier on Monday.
He said Palestinians hurled stones at settlers from neighbouring rooftops and "people here don't believe in turning the other cheek".
Clashes frequently occur between both sides because of a settler enclave established in the heart of Hebron and a further 6,500-strong settlement living in Kiryat Arba on the outskirts of the city.