It happened when agents say a woman armed with a weapon rammed into their vehicle.
On Monday, Chicago Police Superintendent Larry Snelling defended Chief of Patrol Jon Hein, saying there was likely some sort of miscommunication.
Border Patrol Chief Gregory Bovino said he spoke with Snelling, and he does not expect any issues in the future.
Snelling on Monday defended the department's involvement in weekend clashes between federal immigration agents and protesters.
Snelling says at no time did Chief of Patrol Jon Hein tell officers not to respond.
"The chief of patrol would never tell someone to stand down when any law enforcement agency is in trouble or in need of help," Snelling said.