The arrest report on Pedro Bravo, 18, said Aguilar's backpack allegedly was found hidden in the closet of Bravo's home in Gainesville, and blood stains were found in Bravo's sport utility vehicle.
Bravo was denied bail at a court hearing Saturday and remained in jail on a first-degree murder charge.
Bravo and Aguilar, 18, were friends from the Miami-Dade area and were attending school in Gainesville; Aguilar at the University of Florida and Bravo at Santa Fe College.
Aguilar was last seen at a Best Buy store with Bravo on Sept. 20. Prosecutors went ahead with a murder charge on the assumption Aguilar was dead, The Miami Herald reported.
Bravo told police he and Aguilar had gone to Best Buy together and had gotten into a fistfight over Aguilar dating Bravo's ex-girlfriend. Bravo said he beat Aguilar unconscious and left him along the side of a road.
The Herald said a search of the roadside turned up no sign of the missing student.