The Metro Blue Line train station where Deputy Eric Ortiz said the attack took place is near the sheriff's Compton Station.
One male and one female deputy sustained multiple gunshot wounds and are in critical condition.
The suspect is still at large and allegedly sneaked close to the vehicle, shooting through the window and fleeing after, according to FOX 11's Bill Melugin.
Video of the incident, tweeted by LASD, appears to show an individual in dark clothing walking up to the deputies' auto, firing a gun into the vehicle and running away.
The Sheriff's Department also reports protesters blocks the hospital emergency entrances and exits while yelling "we hope they die".
They are currently undergoing surgery and Sheriff Alex Villanueva is at the hospital now.
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The FBI offered resources to the sheriff's department Saturday night as authorities searched for the suspect. He acted as if he was going to walk past the auto, raised a pistol and shot multiple times hitting both deputies, Wegener said.
Both graduated from the academy 14 months ago.
"This is just a sober reminder it's a unsafe job", Villanueva said.
Law enforcement officials were searching for a suspect or suspects after the attack.
LA County Sheriffs' Twitter account posted in the early hours of Sunday (UK time) that they are both "still fighting for their lives". "It pisses me off, it dismays me at the same time".
President Donald Trump tweeted that whoever shot the deputies are, "Animals that must be hit hard!".