Media playback is not supported on this device
Hoey carded two late birdies in the high-pressure event at PGA Catalunya but his level-par 72 left him on three under, which proved two shots too many.
The five-time European Tour winner finished in a share of 37th with only the top 25 and ties earning cards.
Waterford man Gary Hurley finished tied 44th on level par after a closing 72.
As a former European Tour winner, Hoey, 37, can expect to be handed a number of starts next year including a few sponsors' invites.
However, he may opt instead to undertake a full season on the second-tier Challenge Tour which would offer him a more regular schedule.
Hoey's round on Thursday got off to a dreadful start as he bogeyed his opening 10th hole.
The Belfastman was back in contention to win a tour card as he birdied the 12th, 15th and the second but consecutive sixes at the third and fourth saw him drop back to one under.
Three late birdies helped move him back to three under but the damage had been done.
England's Nathan Kimsey led the qualifiers on 13 under after a closing 70.
That left him one ahead of overnight leader Edoardo Molinari plus Scotland's Scott Henry and Argentina's Ricardo Gonzalez.
Amid one of golf's most pressurised environments, there were numerous example of last-day heartache although England's Richard McEvoy just squeezed in on the qualifying mark of five under despite a closing 76.
His compatriot Gary King was the big mover as his closing 66 moved him 39 places up to the qualifying mark.
Michael Hoey missed out on a European Tour Card as two double bogeys wrecked his chances on the final day of the qualifying school in Girona.