Nine other people, including the police officers, were shot and are in good condition, police said.
Police Lieutenant Catherine Buckley said the shooter was armed with some kind of "long weapon" that had a shoulder stock, such as a rifle, and witnesses reported hearing automatic fire.
The alleged gunman was later identified as Robert Lewis Dear of North Carolina. No other details were immediately available.
Authorities said they hadn't determined a motive or whether the shooter had any connection to Planned Parenthood, a national women's health care provider that offers abortions at some clinics.
"We don't have any information on this individual's mentality, or his ideas or ideology," Buckley said.
There had been fears the unidentified gunman might have explosives and police were carefully combing the scene after the siege.
Vicki Cowart, president and CEO of Planned Parenthood Rocky Mountains, said none of her staff or patients had been killed or injured.
Security systems at the clinic included a safe room, in which many people hid during the siege.
"They were able to hunker down and some got out early throughout the afternoon, but those who didn't were in a safe spot," Cowart said.
Joan Motolinia said his sister Jennifer hid behind a table from someone shooting when she called him. "She was telling me to take care of her babies because she could get killed," Motolinia said of the mother of three.
He rushed to the clinic but a police barricade kept him from getting close. "People were shooting for sure. I heard someone shooting. There was a lot of gunfire. She was calm. She was trying to hide," he said.
Police cordoned off the clinic, nearby medical offices and a shopping centre and told people to shelter in place.
Denise Speller, manager of a hair salon, said she heard as many as 20 gunshots in less than five minutes.
She told the Gazette newspaper that she saw a police car and two officers near a Chase Bank branch, not far from the Planned Parenthood clinic.
One of the officers appeared to fall to the ground. The other officer knelt down to help and tried to get the officer to safety behind the car, she said. Another officer told Speller to seek shelter inside the building.
Ambulances and police vehicles lined up at a nearby intersection and police told people via Twitter to stay away from the shooting scene because it was not secure.
Quan Hoang, the owner of a nearby nail salon, told CNN that when he heard the gunfire, he feared a robbery was under way at a bank in the shopping area.
Police told him and his customers to take shelter in the back of his store, and they were still there more than two hours later.
"And we see cops, SWAT, the bomb squad, a whole bunch of people just trying to take cover around the Planned Parenthood area," he said.
Mike Pelosi, who works at a deli nearby, said he heard over the store's loudspeaker just before noon that nobody could leave the store.
The Colorado Springs clinic has been the target of repeated protests and in recent years moved to its current location, which has been derided as a "fortress" by abortion foes.
Hundreds of protesters picketed in front of the clinic in August as part of a push by abortion opponents to cut public funding for Planned Parenthood.
One man was charged with trespassing in 2012 after flouting up to 30 warnings to keep off clinic property, the paper said.
Yesterday's siege ended after a man surrendered to police.
"The perpetrator is in custody. The situation has been resolved," Colorado Springs Mayor John Suthers said. "There's no continuing peril to the citizens of Colorado Springs but there's a huge crime scene to be processed."
