Click on photos below to find out which stars ran
The prince, who usually stands at the finish line to hand out medals to those who complete the 26 mile race, apologised to runners and praised them for their efforts. Harry's message was played on giant screens at the start of the challenge.
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"Good morning everybody," Harry, 29, said. "Congratulations on making it this far to the London Marathon 2014.
"You've all done incredibly well so far to raise as much money as you have and now you're going to have to run for 26 miles around London, which is something that I'm not doing this year and I'm very sad to be missing out.
"But I am hugely privileged to be patron of the London Marathon. So much support, so much effort and so many volunteer hours go into this so hopefully everybody who's taking part and helping will have a really fantastic day. I'm sorry to be missing out but good luck and have fun."
While Harry could not participate in the gruelling race, a host of celebrities took on the challenge, including the prince's old teammates with whom he trekked to the South Pole last December.
Watch Harry's video message below
Actor Dominic West, who formed part of Team Commonwealth during the trek, ran the marathon for charity Walking With The Wounded, and was joined by double amputee Duncan Slater who had been on Harry's team.
British Olympic champion Mo Farah finished eighth, achieving an outstanding time of 2:08:21 — just four minutes after Kenyan world record holder Wilson Kipsang, who crossed the line first in 2:04.27.
Model Amy Willerton and Game of Thrones star Natalie Dormer were spotted posing for a selfie together before the race, while former Made in Chelsea star Hugo Taylor was pictured stretching before the run.
While Tom Daley didn't compete in the gruelling challenge, he cheered on runners from the side and bumped into Wimbledon champion Andy Murray at the finish line.