The video shows the men appearing unarmed and surrendering with their hands raised before being ordered back into a building and then shot.
One of the men reportedly lifted his shirt to demonstrate he was unarmed prior to the shooting.
The Palestinian Authority accused Israeli forces of committing a "war crime" in response to the incident.
The IDF and Israeli police confirmed the shooting near Jenin, stating the men were "affiliated with a terror network", and an investigation has been launched.