With ball in hand Boris Johnson lines up a young opponent Photo: Stefan Rousseau/PA
The young boy hit the ground after coliding with the mayor and was soon up and running again.
He said: "I felt a little bit of pain but it's OK", adding that it had been "enjoyable" meeting the mayor.
After they had picked themselves up, the mayor went over to Toki and asked if he was OK before shaking his hand.
"I'm so sorry," he said.
In a speech to the British and American chambers of commerce in Tokyo, Mr Johnson said: "We have just played a game of street rugby with a bunch of kids and I accidentally flattened a 10-year-old, on TV unfortunately.
"But, he bounced back, he put it behind him, the smile returned rapidly to his face.
"That is my theme tonight - the possibility that confidence can suddenly and unexpectedly return."
Boris Johnson barges into a young rugby player during a game in a Tokyo street Photo: Stefan Rousseau/PA
The game comes as the country's prepares to host the next World Cup in 2019 and marks the end of Boris Johnson's three- day whistlestop trade mission to Japan.
Mr Johnson has been keen to highlight the benefits of staging major sporting events and told the Japanese the 2012 Games left the English capital a "sensational legacy".
He said: "We are both Olympic cities and I have no doubt that Tokyo is ideally placed to take our crown - currently unchallenged - as the city that staged the greatest ever Olympic and Paralympic Games."
Yesterday Mr Johnson said it was "totally unfair" that Japan was knocked out of the Ruby World Cup and the rules should be changed as a result.
Mr Johnson described the team as "heroic" and said it wasn't right that the team had won three matches in a row, but still failed to make it through to the quarter finals.
The boy crashes to the ground as Boris touches down for a try Photo: Stefan Rousseau/PA
Asked if he backed a rule change in the game, Mr Johnson told the BBC: "I'd support that. It seems totally unfair that they should win three times in their pool group and not go through.
Mayor of London Boris Johnson shakes hands with 10-year-old Toki Sekiguchi after the mayor knocked him over during a Street Rugby tournament in Tokyo Photo: Stefan Rousseau/PA
"They are plainly heroes here and they deserve to be. They are fantastically - a fantastic, heroic performance."
He said the Japanese team had "won the hearts" of the British public with their "flair and sportsmanship".
Perhaps Mr Johnson could learn a little from the Japanese when it comes to improving his sportsmanship.
The London mayor has a bit of a track record when it comes to sporting fouls involving small children.
Exactly a year ago, Mr Johnson was forced to apologise after tripping up a small boy during a football match outside City Hall.