Baja California state prosecutor Fermin Gomez said the suspects, Joel Barriga and Alfredo Avila, were captured with seven assault rifles and acknowledged killing the victim.
Ramses Mendoza, 30, was reported missing last week. His bullet-ridden head was found dangling from a bridge Monday, fastened with nylon rope and a metal ring.
Also Thursday, two men were found shot to death in the trunk of a car parked outside the General Hospital in Tijuana. Their hands and feet were bound and their bodies bore signs of torture, according to a state police report.
Gunmen later attacked three men driving past a shopping mall, killing one and wounding the other two.
Cartel-style violence largely abated in Tijuana after the January 2010 capture of Teodoro "El Teo" Garcia Simental, one of two reputed crime bosses allegedly caught up in a bloody turf war in the city across from San Diego.
But Tijuana has seen a series of beheadings, bridge hangings and shootings since President Felipe Calderon visited in October and touted the city as a success story in his four-year-old drug war.
Still, violence remains below levels in 2008, when the turf war reached its peak, and Tijuana is calmer than Mexican cities along the northeastern border.
In the northeastern city of Monterrey, gunmen sprayed a prison Thursday with machine gun fire and hurled at least one grenade that failed to explode. Nobody was injured.
Jorge Domene, a security spokesman for the government of Nuevo Leon state, where Monterrey is located, said the attack was apparently not an attempt to free inmates from the Topo Chico prison, but rather designed to intimidate authorities.
Also Thursday, gunmen shot to death the police chief of the town of Taretan, in western Michoacan state.
Police chief Francisco Aparicio Mendez was driving with his wife and children on a highway when assailants in another vehicle forced him to stop. He got out of his vehicle and was killed by a hail of bullets fired by assault rifles. The assailants then fled, and his family was unharmed.
Taretan is located just south of the city of Uruapan in an area dominated by the La Familia drug cartel, which has frequently attacked police and authorities.