Thomson, from Gosport, had to be rescued by helicopter off his vessel Hugo Boss, after it began taking on water earlier off the Spanish coast.
He had been competing in the double-handed Transat Jacques Vabre race from Le Havre to South America with co-skipper Guillermo Altadill.
The IMOCA 60 yacht had suffered damage two days ago forcing the team out of the race.
They were heading for La Coruna when high seas and strong winds forced them to set off their emergency beacon.
In a statement Hugo Boss said both sailors had been taken back to land safe and uninjured.
Thomson was hoping to race the new yacht in the coveted Vendee Globe round-the-world race in November 2016.
Hampshire sailor Alex Thomson has been rescued from his sinking yacht.