Starting last in a field of 108, Boardman knew his target was the 6:10.38 set by America's George Hincapie. He sprinted up the cobbled climb to finish outside Stirling Castle in a winning time of 6:08.68 - an average of 25.5mph.
Relief and delight were etched on the face of his team manager, Roger Legeay, who had seen his protege's career falter over the last nine months.
"I was so nervous at the start," Boardman said. "I really needed this victory. It came just at the right moment. This may not be the most important race in the world to the other professional teams, but it's given me a golden opportunity to get back to winning form."
Despite being almost unbeatable in prologues last year, Boardman claims to hate the short timed tests. "It's not a pleasant experience, the effort and the pressure are so intense," he said.
The British, in the minority on their own national Tour, had a good day, thanks to the Brite Voice Team, which was competing at this level for the first time.
Matt Illingworth led the Brite boys in fourth place, backed by Jon Clay in seventh, Rob Hayles eighth, Chris Walker 10th and Chris Newton 11th.
The years fell away for Sean Yates who, at 38, was drafted into the Linda McCartney team. Racing internationally for the first time since 1996, Yates was19th fastest, only 28 seconds slower than Boardman.
Although the race distance was short by international standards, all the riders found it a tough proposition, with rough cobbles adding to the hazards of the route.
"It was difficult to judge your pace and leave something in reserve for the last 200 metres," Hincapie said. "The hill was sheer hell." His US Postal squad pipped Brite for the team prize, with the Pole Dariusz Baranowski third fastest and Russia's Viatcheslav Ekimov 12th.
Today, the racing gets serious, with the first road stage proper taking the field 129 miles from Edinburgh through the Borders over Carter Bar to Newcastle.
Boardman, who had played down his chances before the prologue, was equally pessimistic about his prospects for overall success. "My lead is only a handful of seconds and it's going to be very difficult to defend it," he said. "The Continentals are accustomed to eight or 10-man teams, but here there are only six in each team. It makes it almost impossible to control the action. This race is likely to be won in the sprints or a breakaway."
Two of the pre-race favourites for overall victory, the Australians Stuart O'Grady and Neil Stephens, are both well placed in the top 10. O'Grady, who is on Boardman's Gan team, is fifth, 11 seconds behind, while Stephens, the Festina leader, is ninth at 15 seconds.
Ekimov was also expected to be in contention, although he trails by 20 seconds after being troubled by a shoulder injury received in the recent Dunkirk Four Days event.Reuse content