The dead included one police officer and two civilians, Colorado Springs Police Chief Peter Carey told reporters about an hour after the suspect had been captured.
All nine surviving victims - five police officers and four civilians - were listed in good condition at area hospitals, Carney said.
The suspect first engaged in a gun battle with police but ultimately surrendered to officers inside the building about five hours after the start of the violence, which played out under a steady snowfall in Colorado's second-largest city.
A photographer at the scene saw a man in a white T-shirt with his hands cuffed behind his back being taken out of an armored police vehicle and placed in an unmarked squad car.
Police said they did not expect to confirm the suspect's identity before Saturday, but believed he acted alone.
The Denver Post and the Colorado Springs Gazette newspapers, each citing an unidentified law enforcement source, reported Friday night that the suspect was identified as Robert Lewis Dear. The Post gave his age as 57, but neither paper had further details.
The slain lawman was identified as Garrett Swasey, 44, a campus police officer for the University of Colorado at Colorado Springs who joined city police in responding to the first reports of shots fired, authorities said.
Police declined to discuss the gunman's motivations. But the president of the Rocky Mountains chapter of Planned Parenthood, Vicki Cowart, suggested a climate of rancor surrounding abortion in the United States sets the stage for such violence.
"We share the concerns of many Americans that extremists are creating a poisonous environment that feeds domestic terrorism in this country," she said.
Cowart told CNN separately that some of the clinic's staff escaped the gunman by following security protocol and hunkering down in "safe rooms" built into the facility.
The Colorado Springs clinic has been the target of repeated protests by anti-abortion activists, and in recent years moved to new quarters on the city's northwest side - a facility derided as a "fortress" by critics of Planned Parenthood.
The national non-profit group, devoted to providing a range of reproductive health services, including abortions, has come under renewed pressure in recent months from conservatives in Congress seeking to cut off federal support for the organization.
CHECKING FOR EXPLOSIVES
Colorado Springs Mayor John Suthers said authorities were able to help guide the movements of officers through the building by watching live feeds from surveillance cameras mounted inside.
But a city police spokeswoman, Lieutenant Catherine Buckley, said it took officers a number of hours to establish communication with the suspect before he gave himself up.
"We did get officers inside the building. They were able to shout to the suspect and make communication with him and at that point they were able to get him to surrender and he was taken into custody,” Buckley said.
An hour earlier, police said progress in securing the building was slowed by the fact that the gunman brought "some bags" with him into the clinic and left several items outside, all of which needed to be checked for possible booby traps or explosives.
After the arrest, Buckley said it would take hours more, and perhaps days, for investigators to fully process the crime scene.
CNN reported that investigators had located the suspect's car, and the vehicle would be searched for explosives.
Police swarmed the area around the building after an emergency call reporting shots fired at about 11:30 a.m. Mountain Time, and officers ultimately confronted the suspect inside the building, Buckley said.
Television footage aired by CNN showed a number of clinic staff and patients being escorted safely into police vehicles from the building, which lies on the northwest side of Colorado Springs, about 70 miles (112 km) south of Denver.
The FBI and agents from the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives were assisting local investigators.
President Barack Obama was notified of the shooting by his Homeland Security adviser, Lisa Monaco, and "will be updated on the situation as necessary, a White House official said.
DEEPLY DIVISIVE ISSUE
As in much of the rest of the country, abortion is a divisive issue in Colorado, figuring prominently in attack ads during last year’s U.S. Senate race between incumbent Democrat Mark Udall and Republican challenger Cory Gardner, the winner of the election.
At least eight abortion clinic workers have been killed since 1977, according to the National Abortion Federation - most recently in 2009, when abortion doctor George Tiller was shot to death at church in Wichita, Kansas.
Clinics have reported nearly 7,000 incidents of trespassing, vandalism, arson, death threats, and other forms of violence since then, according to the abortion-rights group.
Colorado Springs was the scene of a mass shooting on Oct. 31 in which a gunman killed three people near downtown before dying in a shootout with police.
The city, home to the U.S. Air Force Academy and the U.S. Olympic training center, is also a hub for conservative Christian groups such as Focus on the Family that oppose abortion.
The attack in Colorado sparked jitters across the country. The New York City Police Department reported it had redeployed some of its "critical response" vehicles to Planned Parenthood locations throughout the city. However, it said there were no specific threats to those sites at this time.