A third protester was pushed to the ground as he tried to seize the flame from a British TV presenter taking part in the relay, and police reported 10 arrests in the first hour of the relay.
There were scuffles each time members of the relay team, renowned British athletes and television personalities, handed over the flame to the next runner.
Shouts of "Free Tibet, Free Tibet," echoed around the streets, while demonstrators held up banners and had their faces painted in the colours and style of the Tibetan flag.
Steve Redgrave, former Olympic rower, kicked-off the all-day relay that began at Wembley Stadium under unseasonal snowfall.
"The relationship between China and Tibet will be very much the focus," Jowell told BBC television at Heathrow.
"The pictures of lawful and peaceful protest by people on the route of the torch relay in London will be in marked contrast to some of the scenes that we've seen from China and makes a very clear statement about the importance of freedom in our country."
Publicity for the cause
Redgrave, Britain's greatest Olympian, started the relay of some 80 torch bearers.
"People have realised athletes are a cheap hit, a way to get publicity for whatever cause they're trying to fight for," Redgrave, who won rowing gold medals at five successive Games, wrote in The Guardian on Saturday.
"Sportspeople... should not be misused to make a point."
Among those due to carry the torch were sailor Ellen MacArthur, runner Kelly Holmes, tennis player Tim Henman, footballer Theo Walcott, rugby player Kenny Logan, rower Ed Coode, cricketer Kevin Pietersen, violinist Vanessa Mae, singers the Sugababes, rugby coach Clive Woodward and heptathlete Denise Lewis.
Francesca Martinez, stand-up comedian, withdrew on Thursday in protest over the Chinese crackdown in Tibet.
About 80,000 spectators were expected to view the procession through the city, which was expected to be met by Gordon Brown, British Prime Minister, at his Downing Street residence.
"Meeting the torch is not in any way condoning the completely unacceptable... denial of democracy and freedoms in China," Jowell said.
Brown has brushed aside criticism of his plans to attend Olympic ceremonies in Beijing, insisting it is the right thing to do as London will host the next summer Games in four years time.