Steam fans lined the 35-mile route from Edinburgh, with spectators thronging station platforms, footbridges and fields to watch the 93-year-old engine steam by.
One man stood on the roof of his garage to get a better view, while families spread out picnic rugs beside the Gala Water as they waved to the train.
More than 400 relieved passengers, who had paid up to £169 for tickets, rode in vintage carriages behind the former east coast main line express engine, after the threatened excursion was given the go-ahead with hours to spare.
Network Rail officials worked through the night on Friday to complete safety checks to ensure Flying Scotsman would fit past bridges and platforms, after it was realised the work had not been done.
Transport minister Derek Mackay, who was at Waverley Station in Edinburgh to see the train off, described the blunder as “appalling incompetence”. Network Rail chief executive Mark Carne has promised an investigation.
As the train returned from the Borders to Edinburgh yesterday, a personal apology was relayed to passengers from Mr Carne for Network Rail’s handling of the situation.
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Mr Mackay praised staff from the ScotRail Alliance, which includes Network Rail, for getting the checks completed. The problem is understood to centre on Network Rail’s main office in Milton Keynes.
Mr Mackay said: “I commend those who fixed it at the eleventh hour, but it should not have come to this.
Crowds flocked towards the locomotive as it arrived at Waverley with an ear-piercing whistle. Spectators craned forward to see into the cab, with the driver and fireman’s clothing bathed in orange reflected from the firebox flames.
At 10:46am, with a jolt, Flying Scotsman pulled out of Waverley past a sea of camera phones, steam billowing past the windows and soot scattering over the white linen tablecloths of the first class compartments as passengers dined on asparagus and champagne.
Marcus Roberston, chairman of trip organiser Steam Dreams, announced: “I hope you enjoy the day that briefly was not meant to be.”
Making progress in a far more stately fashion than in its main line heyday, Flying Scotsman reached the current Tweedbank terminus of the line around midday after a brief stop in Galashiels.
A four-hour stopover before its return to the capital enabled people to inspect the locomotive, with delighted children – and older steam buffs – climbing onto the footplate.
Flying Scotsman was last night due to carry a further 440 passengers over the Forth Bridge and around Fife before going on display at Bo’ness Station on the Bo’ness and Kinneil Railway today and returning south tomorrow.
Built in Doncaster, South Yorkshire, in 1923, Flying Scotsman pulled the first train to break the 100mph barrier in 1934. The National Railway Museum in York bought the locomotive for £2.3 million in 2004 before work got under way on its decade-long restoration two years later.