The Ineos Grenadiers rider fell hard in the neutral start of stage three after hitting a stray bidon on a downhill section.
Thomas was able to rejoin the peloton, but the fall had taken it’s toll as the Welshman was dropped on the approach Mount Etna.
By the summit of the climb Thomas had fallen completely out of GC contention, losing 12 minutes to his rivals.
Thomas received medical treatment after the stage and scans revealed has suffered a fracture to his pelvis in the fall.
The team then announced on Tuesday morning (October 6), before the start of stage four from Catania to Villafranco Tirrena, that Thomas wouldn’t be on the start line.
Speaking on Tuesday morning, Ineos Grenadiers Doctor Phil Riley said: “Geraint had an MRI and a CT scan this morning which revealed a small undisplaced fracture in the lower part of the pelvis which wasn’t picked up on the X-rays yesterday. As a precaution he will be withdrawn from the race as it’s an injury that could easily be aggravated.”
Thomas previously abandoned the Giro in 2017 due to injury, pulling out three stages after a crash.
This season has been rough for British WorldTour squad Ineos, as they appeared to be struggling early on in the Criterium du Dauphine.
Egan Bernal than fell dramatically out of contention at the Tour de France and later abandoned the race, leaving the squad’s Grand Tour hopes with Thomas at the Giro.
But it looks like the team have missed another chance at winning a jersey in a three-week race after Thomas’s crash.
The last Grand Tour of the year is the Vuelta a España, where Chris Froome is expected to carry the Ineos leadership in his final race for the team.