The Federal Aviation Administration barred low-flying aircraft from within 3.5 miles of the site.
President Barack Obama was briefed on the explosions by Homeland Security adviser Lisa Monaco. Obama also told Mayor Tom Menino and Gov. Deval Patrick that his administration would provide whatever support was needed, the White House said.
"There are people who are really, really bloody," said Laura McLean, a runner from Toronto, who was in the medical tent being treated for dehydration when she was pulled out to make room for victims.
About two hours after the winners crossed the line, there was a loud explosion on the north side of Boylston Street, just before the photo bridge that marks the finish line. Another explosion could be heard a few seconds later.
The Boston Police Department said two people were killed. Hospitals reported at least 57 injured, at least eight of them critically.
A senior U.S. intelligence official said the two other explosive devices found nearby were being dismantled. The official spoke on condition of anonymity because he was not authorized to discuss the findings publicly.
Competitors and race volunteers were crying as they fled the chaos. Authorities went onto the course to carry away the injured while race stragglers were rerouted away from the smoking site.
Roupen Bastajian, a 35-year-old state trooper from Smithfield, R.I., had just finished the race when they put the heat blanket wrap on him and he heard the blasts.
"I started running toward the blast. And there were people all over the floor," he said. "We started grabbing tourniquets and started tying legs. A lot of people amputated. ... At least 25 to 30 people have at least one leg missing, or an ankle missing, or two legs missing."
Smoke rose from the blasts, fluttering through the national flags lining the route of the world's oldest and most prestigious marathon. TV helicopter footage showed blood staining the pavement in the popular shopping and tourist area known as the Back Bay.