Thousands lined the streets to see the 36,000 runners set off from Blackheath, where a 30-second silence was held.
Three people were killed and more than 170 others injured by the Boston Marathon’s twin blasts at the finish line.
Hundreds of extra police officers were drafted in as reassurance in London.
About half a million people were expected to watch the race, although official estimates have yet to be made.
Just before the start of the main race, event commentator Geoff Wightman introduced the half-minute silence.
“Marathon running is a global sport,” he said.
“It unites runners and supporters on every continent in pursuit of a common challenge and in the spirit of friendship and fellowship.”
Geoff Wightman said the marathon family had been “shocked and saddened” by the events in Boston and the silence was to show “our respect and support for the victims”.
A senior US diplomat based in the UK said the commemoration underlined the “special relationship” between the two countries.
Barbara Stephenson, Charge d’Affaires at the US Embassy, told Sky News: “We’ve had responses from Her Majesty the Queen, all through Twitter from the British people, and now we have got tens of thousands of London Marathon runners wearing a black ribbon in solidarity with the people of Boston.
“As my senior law enforcement person said on Friday afternoon, it’s moments like this when you know what the special relationship’s really all about.”
London Marathon appears to have passed off without incident.
Race director Hugh Brasher said before the race that a full security review had taken place and everyone had been adamant that the “show must go on”.
The Metropolitan Police in London said it had reviewed security plans after the Boston attacks and that the extra officers would be used for “for reassurance patrols”.
Australia’s Kurt Fearnley was the first athlete to cross the line, winning the men’s wheelchair race.
Tatyana McFadden won the women’s wheelchair race less than a week after winning the equivalent race in Boston.
She said: “You know this whole weekend was dedicated to Boston and we got huge support from London. So, I couldn’t be happier – just getting support. It was just a wonderful day.”
In the women’s elite race, there was controversy early on when 2010 wheelchair winner Josh Cassidy dropped out after a collision with Olympic champion runner Tiki Gelana.
She continued running but was off the pace and her race was won by Kenyan Priscah Jeptoo in a time of 2:20:15.
The men’s race was won by Ethiopia’s Tsegaye Kebede and the men’s race by Ethiopian Tsegaye Kebede, who overtook 2011 champion Emmanuel Mutai in the closing stages.
Mo Farah, who won the 5,000m and 10,000m at the 2012 London Olympics, ran only the first half of the 26.2-mile course.
Afterwards he praised the atmosphere of the crowd and said the experience was good practice ahead of him running the full race next year.
Singer Katherine Jenkins, cricketer Andrew Strauss and McFly’s Harry Judd were among the well-known names running.
Prince Harry, who is the patron of the London Marathon Charitable Trust, gave the winners their medals.
He said it was “never an option” that he would not be at the race because of security fears following the Boston bombings.
“The great thing about the marathon is no matter what color you are, or religion, no matter what nationality you are, everyone comes together to run a certain distance to raise money for amazing causes.
“I think that you can never that take away from people.”
Meanwhile, specialist US terrorism officers are waiting to question Dzhokhar Tsarnaev, the surviving suspect in the twin bombings close to the finish line of the Boston Marathon.
Dzhokhar Tsarnaev’s older brother, Tamerlan, died after a shoot-out with police.
Virgin London Marathon has pledged to donate £2 ($3) for every runner that finishes Sunday’s event to The One Fund Boston set up to raise money for victims of the explosions.
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