The game was settled six minutes from time when Irish turned the ball over and Jacobs broke clear to send Varndell in unchallenged.
And they had to survive a late onslaught from Irish deep into overtime as the ball stayed alive.
Scotland, playing with the strong breeze, were putting together some excellent passages of keep-ball which had the Irish defence scrambling.
Neither side had really threatened a try and when one arrived it was courtesy of a penalty try as the Irish pack tried to steamroller the ball over the line.
Noon showed great skill in chipping the ball over the onrushing Irish defence as he made inroads down the right touchline while Tait, back on for Sackey, was also a thorn.
Irish debutant Conor Henderson - another ball-playing midfielder - probed for a gap through the back-line and the 19-year-old's deflected pass was pounced on by Tomas Rosicky, who sped to the byeline to clip a square ball through the legs of Charlie Daniels across the box.
"Our line-outs did not fire and we could not deliver the type of ball we needed, " said the Irish coach.
First Tagicakibau danced around two defenders for his first try just minutes after coming off the bench and then Stowers slammed the ball into the base of the post to score his as Irish appeared to kill off the contest and threatened to run riot.
Despite having an extra man, it was London Irish's last hurrah and they finished the match with Steven Bachop scrambling the ball away from underneath his own posts.
But a crafty line-out move caught the Irish flat-footed as Mike Phillips broke away to score, though Wales had used a different ball at the line-out.
The Irish did cross the Fiji line for the first time in the 18th minute as Jamie Heaslip picked up the ball from the scrum and found Eoin Reddan, who fed Earls to burst through the Fiji rearguard and under the posts to complete a well executed move, converted by Sexton.
Northampton full-back Ben Foden, a renowned runner with ball in hand, had been tipped to start against Scotland but Johnson has retained his faith in London Irish number 15 Armitage.
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