The two suspects - Angel Joseph Uriate, 35, and Noah David Beard, 25 - were taken into custody by sheriff's deputies and federal agents after being under around-the-clock surveillance since Jan. 23, Tulare County Sheriff Mike Bordreaux said.
Uriate was injured in a gun battle with agents of the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives (ATF) after he opened fire on officers as they approached him in Goshen, California, the town where the killings took place on Jan. 16, Bordreaux said.
He underwent surgery at a local hospital and was expected to survive, the sheriff said in a news conference announcing the arrests. Beard was captured in nearby Visalia without incident, Bordreaux said.
Last month's carnage raised the profile of rising gang violence and drug trafficking in some of California's more rural, isolated areas, as a state known for some of the strictest gun laws in the country faced a spate of deadly mass shootings.
The Goshen murders came one week before the first of two more highly publicized rampages by gunmen in California that left a total of 18 victims dead in the Los Angeles suburb of Monterey Park and the San Francisco Bay-area coastal town of Half Moon Bay.
By comparison, authorities said, the violence in Goshen was more calculated and deliberate.
"This was clearly not a random act of violence," Bordreaux said. "This family was targeted by cold-blooded killers." Many of the victims died of gunshots to the head.
The sheriff described both suspects as members of the Nortenos, a primarily Mexican-American gang network affiliated with the prison-based criminal organization known as Nuestra Familia, Spanish for "our family."
Bordreaux said two members of the victims' family were also "well-known, validated" members of the rival Surenos gang.
"This case is very dark, it comes from a very dark place," ATF special agent Joshua Jackson told reporters.
A criminal complaint filed by county prosecutors on Friday charged each suspect with six counts of murder, as well as firearms felonies, in the shooting deaths.
The attack, carried out on a residential property occupied by nine people, most of them family members, struck fear in a rural agricultural community of about 5,400 residents roughly midway between Los Angeles and San Francisco.
Bordreaux said chilling video footage discovered by investigators showed one victim, a 16-year-old mother, running with her 10-month-old son clutched in her arms as she tried to escape the shootings. She hurriedly lifted the infant over a fence and placed the baby on the ground on the other side, then scaled the fence herself, before both the child and the mother were shot dead, according to the sheriff.
The teen mother's 72-year-old grandmother was also among the slain. Two women on the property survived by hiding in a trailer.
Bordreaux said the two suspects were identified and placed under 24-hour surveillance starting a week after the killings, and authorities kept close tabs on both men until investigators had gathered sufficient evidence to charge them.
Bordreaux said the pair are suspected of being the sole perpetrators of the killings, and that the massacre is believed to have stemmed from organized gang activity, though a precise motive remained undetermined. Authorities identified Beard as the suspect accused of physically shooting the 16-year-old girl and her infant son.
The investigation, which involved searches and questioning of inmates in several state prisons, was continuing with assistance from various local law enforcement agencies, state police, the California corrections department, the FBI and ATF, officials said.