The torch was on the side of Paralympic badminton hope David Follett's wheelchair in Great Torrington, Devon when it went out.
The torch's design had been tested at BMW's climatic centre in Munich to ensure it could stay alight in all weather conditions.
Luckily there was a replacement flame inside the vehicle convoy that accompanies it along its route.
The replacement was also lit in Olympia, Greece at the torch lighting ceremony.
"The flame went out due to a malfunctioning burner. It is not uncommon for a flame to go out and this can happen for a number of reasons, for example in extreme winds," said a spokesperson for organisers Locog.
"We keep the mother flame in specially designed miners' lanterns so if the flame does go out for some reason on the relay we re-light it from the source of the flame."
Last week torch designers Edward Barber and Jay Osgerby said they were confident that it would be able to cope with all conditions on the route.
"The torch had to be economical and sustainable as well as being beautiful and strong, so it’s an incredibly complicated piece of design," they said.
"It has to function at high altitudes, sub-zero temperatures, in strong winds and also be incredibly light as so many different types of people will be carrying it."
Monday's leg of the relay will see 113 people carry the Olympic torch over 135 miles (217km).
Some 8,000 people are due to take part around Britain and into Ireland before the cauldron is lit at the opening ceremony on July 27.