The protests erupted after a man died in a queue on Monday waiting for security checks for workers entering Israel.
"We have the right to work in dignity without being humiliated," read a banner waved by labourers who blocked the Erez Crossing to protest against stringent Israeli security procedures.
A Palestinian construction worker, 41-year-old Muhammad al-Shaikh, collapsed and died a day earlier as he waited among a crowd of thousands of Palestinians in the early hours of the morning to enter Israel for work.
The Israeli army said al-Shaikh died of a heart attack at the crossing, where security measures were tightened after a Palestinian woman posing as a worker blew herself up, killing three people last month.
"We get to the other side of the checkpoint very tired and hardly able to work"
Ahmad Abu Mahir,
About 17,000 Gazans file through the Erez Crossing every morning for work in Israel, where they earn about 200 shekels a day ($45), three times the amount they would earn in the Gaza Strip where unemployment is rife.
"(We) wait here until the soldiers begin receiving workers at 2am and then we come out after inspection at 8am," said one worker, Ahmad Abu Mahir.
"We get to the other side of the checkpoint very tired and hardly able to work."
Hospital officials in Gaza said they treated about seven workers every day for breathing problems and bruises suffered while standing in pressing crowds in a narrow passage for hours, waiting to pass through the checkpoint.
The Israeli army says security measures are needed at the border to prevent resistance fighters from crossing into Israel.