The protesters in an affluent neighbourhood of Amman carried Palestinian flags and chanted: "They said Hamas is terrorist. All of Jordan is Hamas"
There was no immediate Palestinian comment on the incident, which occurred at a roadblock between Israel and the central West Bank, near the city of Tulkarem.
The injured Israeli guard was being treated at Sheba Medical Center, in Tel Aviv, and was expected to survive, the defence ministry said in a statement.
The alleged Palestinian attacker was 16 years old, it added.
Violence has simmered in the West Bank, part of territory Israel captured in the 1967 Middle East war and that Palestinians seek for a future state, since US-sponsored peace talks broke down in 2014.