Flanagan had led the women for the first 20 miles of the 26.2-mile (42.2-km) race, setting a punishing pace, before dropping back and finishing seventh.
"I love Boston so much and I really wanted to do it for this city," said a tearful Flanagan, who was raised in Marblehead, Massachusetts. "I'm so sad I couldn't do it for Boston."
Last year, three people, including an 8-year-old boy, were killed and 264 were hurt when, prosecutors say, a pair of ethnic Chechen brothers left homemade bombs at the crowded finish line, tearing through the crowd.
Buzunesh Deba of Ethiopia was second and compatriot Mare Dibaba third. They too turned in faster performances than the previous course record of 2:20:43 set in 2002 by Margaret Okayno of Kenya.
- Athletics, Track & Field