The man, who has not been named, was given medical attention immediately after finishing the race, but was pronounced dead at hospital.
A spokeswoman for Virgin Money, the event's organiser, said: "The organisers of the Virgin Money London Marathon would like to express their sincere condolences to the family and friends of the deceased.
"Our thoughts and deepest sympathies are with them at this difficult time."
It is the first death in the event since 2012, when 30-year-old hairdresser Claire Squires, from North Kilworth, Leicestershire, collapsed a mile from the finish line and died later from cardiac failure.
She was raising money for the Samaritans and in the week after her death donations to her fund-raising website jumped from £500 to more than £1 million.
An estimated 36,000 people took part in yesterday's race, the 34th London Marathon, from elite athletes to fun runners raising money for charities.
More than 1,200 volunteers from St John Ambulance lined the streets and medical staff advised runners to take on plenty of water and keep well hydrated as the race got under way under near-cloudless skies.
Temperatures of 11C (51.8F) were recorded at the start of the race in Greenwich at 10am, but as runners made their way around the 26.2-mile course through the capital the bright sunshine and lack of a breeze made conditions feel considerably warmer.
By the time runners reached the finish line in St James's Park temperatures reached 16C (60.8F), the equal highest of anywhere in the UK.
Kenyan world record holder Wilson Kipsang won the men's race in 2hrs 4mins and 29secs, a course record, while home favourite Mo Farah came home almost four minutes back in 2hrs 8mins and 21secs.
The women's title was taken by Edna Kiplagat of Ethiopia, in a time of 2hrs 20mins and 21 secs.