Rotherham’s Thomson finished with a final round of 69 at Lumine having previously shot 67 72 68 67 71 in a marathon test of nerve and skill.
It was good enough for a tie for 18th place as the top 25 plus ties – 33 players in all – claimed playing privileges on the European Tour.
But Howley Hall’s Marcus Armitage, looking to regain his playing card after finishing 152nd with winnings of €168,137 after this, his maiden season, finished agonisingly one shot short.
“It’s not really hit home yet. It’s so emotional, it’s been such a long journey for us to get to this point and it’s hard to let it all sink in,” said 21-year-old Thomson, who – between the ages of seven and 12 – endured extensive chemotherapy treatment to combat acute lymphoblastic leukaemia, which went into remission.
“My dad’s (Nigel) been here with me through it all. It’s been some tough times, but here we are and it’s great. We had a hug and a tear on 18 and I’m looking forward to getting a beer now.
“I’ve come through all three stages – I got in on the mark in First Stage and then a play-off in Second Stage and now I’m a European Tour member, so it’s been a hell of a journey.”
Thomson’s chances seemed to be slipping away when he bogeyed three of the first five holes on the back nine after turning in three-under-par 32. But two pars followed and then crucial birdies at 17 and 18.
He was already assured of a Challenge Tour card by playing all six rounds of Final Qualifying after the disappointment of just missing out on gaining one through his season on the EuroPro Tour. He placed ninth, just £3,500 short in winnings that would have earned a top-five place on the Race to Amendoeira and with it a card.
But now Thomson – known affectionately as Jigger – can look forward to pitting his skills against Europe’s elite having already tested the waters with two appearances this year.
He received an invitation to play in the Czech Masters in September and began the final round in the penultimate group before falling away to 54th place.
Three weeks later he shared 25th place, alongside three-time major winner Padraig Harrington, in the Portugal Masters.
It means he will start his campaign as a fully-fledged, card-carrying member of the European Tour with some vital experience under his belt.
Standing at 6ft 9ins, Thomson is the tallest player to have competed on the top-tier tour, and was quick to make a big impression on the EuroPro Tour, winning the Glenfarclas Open in September 2016 just four weeks after turning professional.
In a distinguished amateur career, as well as earning county honours Thomson played for England and in 2015 won the George Henriques salver awarded to the leading Great Britain & Ireland player aged under 20 in the Brabazon Trophy, which was held that year at Notts (Hollinwell), where he also had the lowest score, 66, of the week.
Armitage carded a superb 66 to close at Lumine after earlier scores of 71 71 74 68 66.
Four birdies and an eagle at the second had him on six under for the day and 13 below par overall, which would have been good enough to claim a card.
But his only bogey of the day, at the 15th, proved his undoing.