Desiree "Desi" Linden, 34, became the first American woman to win the women's race since Lisa Larsen Weidenback did so in 1985 after pulling away from a competitive field and battling unusually cold, wet and windy conditions. American Tatyana McFadden, won the women's wheelchair race for the fifth time, wore two jackets, with a layer of plastic between them and hand warmers against her chest.
Only a few kilometres into the race, Flanagan had to drop out of her lead position for an an emergency toilet stop.
The drought is over for American women at the Boston Marathon.
Whether or not fans knew the significance of Linden's effort, the lined streets near the finish were packed with screaming fans.
For her part, Flanagan finished in seventh, 6:37 down on her pacesetting pal. "I'm thrilled to be here and get it done".
Watch the incident play out in the video at the top of the page.
Sportsmanship among the Americans was on full display during the race, particularly when Linden held back toward the beginning of the race to help Flanagan catch up to the pack after stopping at a port-a-potty.
Linden overtook Ethiopia's Mamitu Daska and Kenya's Gladys Chesir at Heartbreak Hill after the 32km mark and kept the lead from there to win in 2:39:54. Canadian athlete Krista Duchene finished third, at 2:44:20.
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For more than 20 years, the first man and woman across the Boston Marathon finish line have nearly always been athletes from Kenya or Ethiopia.
"I love this city, this race, this course".
"This is a race the entire city cares about".
Correction: The original version of this story misstated the amount of time by which Desiree Linden lost the 2011 Boston Marathon.
The race marked five years since the Boston Marathon bombing tragedy in which two explosions near the finish line killed three people and wounded more than 260.
On the fifth anniversary of the finish line explosions that killed three and wounded hundreds more, Linden and Kawauchi led a field of 30,000 runners through a drenching rain, temperatures in the mid-30s and gusts of up to 32 miles per hour on the 26.2-mile trek from Hopkinton.
Weather conditions were so bad the Boston Red Sox, who usually play a Major League Baseball home game on race day, postponed their Fenway Park contest for the first time since 1984.
Yuki Kawauchi passed defending champion Geoffrey Kirui as they passed through Kenmore Square with a mile to go to win the men's race in 2:15:58 and earn Japan's first Boston Marathon title since 1987.
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