Joshua Komisarjevky, 26, of Cheshire, and Steven Hayes, 44, of Winsted, were formally charged with assault, first-degree aggravated sexual assault, kidnapping, burglary, robbery and arson. They were each ordered held in lieu of $15 million bond.
State police have said that additional criminal charges are likely to be filed.
The two men, both in orange prison jump suits and shackles, did not enter pleas, and answered only, "yes," when asked if they understood their rights.
Jennifer Hawke-Petit, 48, and her daughters, 17-year-old Hayley Petit and 11-year-old Michaela were found dead Monday in their burning home after the family had been held hostage for hours. The father, Dr. William Petit Jr., 50, was the sole survivor.
Komisarjevky and Hayes were caught fleeing from the burning home, an apparent attempt to cover their tracks. The gold Chrysler Pacifica SUV they were driving rammed three police cruisers, but no police officers were injured.
Neighbor Walter Ryan was walking his dog when he saw the flames coming from the home and then watched as police, with guns drawn, moved through yards and shouted, "'Get out of the car!'"
Police said they were tipped off that the family was in danger by employees at a local bank when one of the suspects accompanied a female hostage to make a withdrawal around 9:30 a.m. Bank employees became suspicious and called police who drove to the Petit home in the quiet suburb.
The Hartford Courant says the female hostage at the bank was Hawke-Petit, who may have alerted the bank employees somehow.
Dr. Petit, a prominent endocrinologist, was severely injured, but escaped the burning home and managed to tell police what happened. According to the Courant, he had been beaten in the head and left tied up in the basement, but hopped up the stairs to escape the fire.
He was reported in stable condition at a local hospital.
"It's devastating. What I understand so far is that just the husband that survived, and as a father and husband myself, I can't imagine living that way," neighbor Chad Wilson told CBS affiliate WFSB-TV.
A bail commissioner said Hayes and Komisarjevky each have records that include more than 20 prior burglaries. Both had been out of prison on parole.
Sources from the state Department of Correction told WFSB the two men recently lived in the same halfway house following their releases from prison.
"In Cheshire we're not used to this type of event," Police Chief Michael Cruess said. "It's a very unfortunate, tragic event that's probably going to reach right down to the core of the community."
"I'd like to think it was an isolated incident," Matt Eigner, who lives down the road, told the Waterbury Republican American. "I'm scared to death, it's unbelievable."
"It is a shocking day for everyone. It's just beyond anyone's understanding," said Larry Tanner, president and chief executive officer of The Hospital of Central Connecticut.
Petit is the medical director of the Joslin Diabetes Center Affiliate at The Hospital of Central Connecticut in New Britain. His wife of 22 years was a nurse and worked at the Cheshire Academy, a boarding school, as co-director of its health center.
Their upper-middle class neighborhood includes colonial homes with well-kept lawns in the New Haven suburb.
The Rev. Ronald A. Rising, a neighbor, said he has known the family for more than 10 years.
"They're just a lovely family," he said. "It's just awful to think it would happen to a family like that in this community. You don't think about those things happening."
Neighbor Laura Parisi, a friend of the Petits' older daughter, Hayley, said the 17-year-old had just graduated from the prestigious Miss Porter's School in Farmington and had been accepted at Dartmouth, her father's alma mater.
"It's just insane," Parisi said of the deaths. "I can't even describe it."
Officials at Miss Porter's School told WFSB that Hayley ran a charity called Hayley's Hope which raised more than $50,000 to fight multiple sclerosis. She was also co-editor in chief of the school newspaper, co-captain of the crew team and a member of the basketball and cross country teams.
Her mother had been diagnosed with multiple sclerosis eight years ago, the Courant reported.