The double Olympic champion, who won 5,000m and 10,000m gold at the London 2012 Olympics, tripped up during the race and later collapsed a second time after crossing the finish line.
In dramatic scenes, Mo fell to the floor and was reportedly unconscious for about three minutes. He was given emergency medical treatment and assisted into a wheelchair as his wife Tania bent down at his side.
"Hi guys... I'm doing ok... thanks for the concern... disappointed with today... I gave 110%... couldn't do anymore... sorry guys...," the father-of-three posted on Twitter.
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Mo spoke to reporters after the race, insisting that he was fine and trying his best to put on a brave face.
"I do remember sort of passing out," he said, smiling and looking relaxed. "I tried so hard in the race, taking a fall and then going through. But, yeah, I'm all right. It's fine. It's not a big deal."
Mo was held back at the six-mile mark when he tumbled to the ground after one of his heels was clipped. The athlete got back up but said that for the last four miles he ran "seeing stars".
"I'm not sure what happened," said Mo. "I just remember sort of falling down and just hitting the ground quite hard. I got caught on my hip, my ankle, the whole right-hand side."
The Somali-born hero completed the 13.1 mile race in 61 minutes and eight seconds, finishing just 18 seconds after the winner — two-time champion of the New York marathon Geoffrey Mutai from Kenya.
Mo had been hoping to finish first and beat his personal best of 60 minutes 59 seconds which he achieved last year.
"It would have been nice to win today, but he (Mutai) is a good athlete," said Mo. "Nothing changes for London — I will just keep training."
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Spokesmen for the Olympic champion blamed the incident on the difference in climate between a cold New York and a hot Kenya where Mo had been training for two months.
"Conditions today were very cold," he added. "London's going to be different, but I felt good up to the point I went down. It happens in the race. You've just got to deal with it."
Mo will return to train in Kenya next week, before he takes on the challenge of competing in the Virgin Money London marathon on 13 April.