those killed and wounded by the blasts in the United States.
Security for the London race was tightened in the wake of the Boston carnage last Monday, with several hundred extra police officers drafted in along the 26.2-mile (42.2-kilometre) course.
The event was dedicated in many other ways to the Boston attacks.
After the participants, Olympic athletes among them, bowed their heads for the half-minute silence, they raised a huge cheer.
The runners then set off on a course over which hung many banners, including one reading: "Run if you can, walk if you must, but finish for Boston".
Organisers announced that £2 ($3, 2.30 euros) for every finisher would be donated to a fund for the Boston victims.
There was also a social media campaign encouraging runners to place their hands on their hearts as they crossed the finish line.
"Marathons are all about people coming together," Keith Luxon, an amateur runner who competed in the Boston race and was also due to take part in London, told the BBC.
"Part of that was ruined in Boston, and it's up to us to put some of that back."
The twin blasts by the Boston finish line killed three spectators, including an eight-year-old boy, and left around 180 people with often severe injuries.
US police on Friday captured a 19-year-old ethnic Chechen, Dzhokhar Tsarnaev, suspected of carrying out the Boston attacks with his brother, after a desperate manhunt that virtually paralysed the city. He remains in a serious condition in a Boston hospital.
British organisers estimated that more than 700,000 spectators lined the marathon route in London and many said the horrors in Boston had made them more determined to show their support.
Katie Prahin, who lives in London but comes from the US state of Virginia and studied in Boston, was among those cheering on the runners.
"It is good to be here today and not shying away," the 35-year-old social worker told AFP.
"The silence at the start of the race was a nice way to show respect and support."
Marshals in high-visibility jackets were dotted along the route and police officers on bicycles slowly patrolled behind the spectators, while a sniffer dog was walked along the course in the city centre.
London Marathon chief executive Nick Bitel said that "obviously with the shocking pictures (from Boston), it galvanised us into having a look at our security measures."
But while security was boosted, no additional threat was detected.
"We've had to make a few changes and put some new security measures in, but we've had such an amazing response from the runners and the public," Bitel said.
The marathon course snaked past famous London landmarks including Tower Bridge, St Paul's Cathedral and the Houses of Parliament before finishing in front of Buckingham Palace.
In the men's race, Ethiopia's Tsegaye Kebede chased down 2011 champion Emmanuel Mutai to win in 2hr 06min 04sec.
The women's race was won by Kenya's Priscah Jeptoo, who surged clear to claim victory in a time of 2hr 20min 15 sec, with compatriot Edna Kiplagat in second place.
Tatyana McFadden of the United States won the women's wheelchair race after also winning it in Boston.
She told the BBC: "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."
Prince Harry, who presented the medals to the winners, said the response of the crowd and runners in London to the Boston attacks had been "fantastic" and "typically British".
He added: "The way Boston has dealt with it has been absolutely remarkable and it was never going to stop anyone down here."