The Welshman came off his bike around 30 kilometres from the end of stage four and received medical attention at the side of the road.
However, the 33-year-old reassured fans that he will be on the start line in Brussels on July 6 with a positive update on Wednesday morning.
Thomas wrote on Twitter: "Thanks for all your messages!! Gutted to leave tds but luckily I'm all ok.
"I hit my head and needed stitches above my eye, so the doctors stopped me getting back on my bike. It just means I'll need some big training rides next week now."
Thomas also "suffered abrasions on his shoulder" but no significant injury after passing an initial concussion roadside test and returned to the team hotel on Tuesday evening following further scans and X-rays at a local hospital.
"There was a lip in the road that came out of nowhere," Thomas said on teamineos.com about the incident.
"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."
Thomas is due to lead Ineos at this year's Tour after team-mate Chris Froome crashed while in France for the Criterium du Dauphine last week.
Froome underwent extensive surgery following his high-speed crash, which left him with multiple injuries, including a broken femur.