Israeli troops in four vehicles rushed to the scene and fired teargas as teenagers climbed aboard a bulldozer and hurled stones at them.
Other protests were planned to mark four years since the International Court of Justice (ICJ) issued a non-binding resolution calling for parts of the barrier built inside the West Bank to be torn down - and construction to be halted along the planned route inside the territory.
"Our goal is to stop the bulldozers," al-Khawaja, who is also one of the organisers of weekly protests staged at the construction site, said.
"The goal of the protests is peaceful," he added, while admitting that there had been incidents of rock-throwing.
"What do they expect from farmers who see their trees are being uprooted? They want to live, they want to send their children to university."
Hassan Musa, 33, a Palestinian schoolteacher who attended the protest with his seven-year-old son, said: "The building of the wall affects everyone's life. They want to expel us from our land."
Israeli authorities say the barrier is needed to stop potential attackers from infiltrating Israel and Jewish settlements in the West Bank.
However, Palestinians denounce it as an "apartheid" wall aimed at grabbing their land and undermining the viability of their promised state.
Israel has pressed ahead with construction of the barrier and completed about 200km since the ICJ issued its order.
To date Israel has built 57 per cent of the projected 723km of steel and concrete walls, fences and barbed wire, according to UN figures.
When completed, 87 per cent of the barrier will be built on West Bank territory which Israel occupied in 1967, according to the Office for the Co-ordination of Humanitarian Affairs.