The Welshman came off his bike around 30 kilometres from the end of stage four on Tuesday and received medical attention at the side of the road.
Team Ineos reported the 33-year-old remained conscious following the incident and was taken to hospital for further checks, sport director Gabriel Rasch had said.
Later on Tuesday, it was confirmed Thomas had "suffered abrasions on his shoulder and a cut above his right eye", but no further significant injury.
"There was a lip in the road that came out of nowhere," Thomas said. "An Astana rider hit the lip and crashed and I had nowhere to go. I landed on my shoulder and my face and there was quite a bit of blood.
"You've always got to be cautious with a head injury, and whilst I was keen to carry on, the doctors made the right decision to pull me out of the race."
Team Ineos added Thomas' planned involvement in the Tour de France "isn't likely to be affected by today's crash".
Thomas said: "Clearly it's frustrating and a small setback for my Tour de France preparations, but there's still plenty of time before we start in Brussels in a few weeks' time.
"We will re-calibrate and I'm sure my coach Tim (Kerrison) will have a plan in place to ensure I'm ready for July 6th."
Thomas is due to lead Ineos at this year's Tour, which takes place next month, after team-mate Chris Froome last week crashed while in France for the Criterium du Dauphine.
Froome underwent extensive surgery following his high-speed crash, which left him with multiple injuries, including a broken femur.
Team Ineos doctor Derick Macleod gave some more details surrounding Thomas' crash.
"Geraint took a heavy fall. The main area of impact was to his head. He passed his initial concussion roadside test, but with the nature and severity of the impact, it was felt unsafe for him to continue in the race," Macleod said on the team's website.
"He was taken to hospital and thankfully all the X-rays and scans have come back clear. He's now back in the team hotel and in good spirits."
Macleod added: "He's been given the all clear which is great, but we will continue to monitor him over the next few days.
"Knowing Geraint, it won't take him long to get back on his bike, but we'll need to ensure he's symptom-free in the next few days before he does so.
"We're optimistic he'll make a full recovery over the coming days though and - all being well - he'll be back on his bike very soon."
Deceuninck-Quick-Step rider Elia Viviani went on to claim the stage win in Switzerland following a sprint finish in Arlesheim ahead of Michael Matthews (Sunweb) and overall race leader Peter Sagan of Bora-Hansgrohe.
Viviani was set up by good work from team-mate Michael Morkov during the closing 1.5kilometres, the Italian staying close to the barriers on the left, while Matthews was able to outpace Sagan in the dash for the line.
Sagan retains the overall lead, ahead of Australian Matthews by 10 seconds, with Kasper Asgreen (Deceuninck-Quick-Step) in third.