Despite losing 1-0 to the Icelandic champions, Akranes, the Scots' 3- 1 first-leg victory was enough to see them through.
And Thomson played a bigger part than most, turning aside shots from all angles as Akranes totally overran a ragged Raith side.
Manager Jimmy Nicholl sent his team out in an ultra-defensive formation, employing two markers to cope with the twin threat of Bjarki and Arnar Gunnlaugsson, in addition to a solid flat-back four.
And even then they needed a huge portion of luck to hold on to their European dream.
As early as the fifth minute Bjarki Gunnlaugsson had a shot deflected off target and his twin brother Arnar headed wide after a great Haraldur Ingolfsson cross seven minutes later. Ingolfsson also volleyed wide as Akranes finished the first half well on top.
But Raith's luck ran out six minutes after the break when Hognason rose unchallenged to head an Ingolfsson corner goalwards and Arnar Gunnlaugsson diverted the ball past Thomson with a diving header from a couple of yards.
Akranes went in search of a second goal to kill the tie, but Thomson stood firm,pulling off breathtaking saves from Olafur Thordarson and Jonsson.
Akranes: T Thordarson; Haraldssan, Hogneson, Jonsson, Adolfson, Miljkovic, B Gunnlaugsson, Gislason, A Gunnlaugsson, O Thordarson, Ingolfsson.
Raith Rovers: Thomson; McAnespie, Broddle, Coyle, Dennis, Sinclair, Kirkwood, Cameron, Crawford, Lennon, Dair.
Referee: R Luinge (Neth).