Both have denied involvement in the crime.
Authorities also have not named the pair, also accused of stealing and selling Aguilar’s Jeep and going on a spending spree with his credit cards.
Police said some of the man’s other belongings were still in their possession at the time of their arrests.
Aguilar, a city firefighter and paramedic for 20 years, vanished Aug. 20 after traveling to his condominium near Rosarito, according to reports.
Investigators said Aguilar was lured there that day by a woman he knew.
Unbeknownst to Aguilar, he unwittingly agreed to a meeting where he would be kidnapped for ransom, CBS reported.
The plot fell apart when Aguilar tried to escape, police said.
Not long after Aguilar arrived at the rendezvous, a van screeched on the scene.
Aguilar panicked and attempted to run, but was cut down after a gunman emerged from the vehicle, police said.
The suspects apparently fled the scene with the victim.
At some point during the ordeal Aguilar died, police said, although it’s not clear whether the gunshot killed him.
Los Angeles Fire Chief Ralph Terrazas expressed condolences to Aguilar’s family, CBS reported.
“This is a tragic outcome to a case we were hoping would end differently,” Terrazas said in a statement, according to the network. “On behalf of the men and women of the LAFD, we send our deepest condolences to Firefighter Aguilar’s family and we stand ready to assist them in the days to come.”
The investigation is continuing, and authorities said they are seeking one other suspect in the case.