The Welshman of Team Sky allegedly rode onto a roadside bike path behind some spectators before the second pass of the Oude Kwaremont with 56km left to race.
The Tour of Flanders' official Twitter feed confirmed that Rowe had been withdrawn from the race, saying simply "@LukeRowe1990 has been taken out of the race by the race jury! #RVV #RVV18".
Team Sky replied to the tweet, saying: "Sad to see @LukeRowe1990 will be forced out of the race. Looked like he got caught out by spectators while trying to move up ahead of the Kwaremont."
Rowe himself added a statement to Twitter after he withdrew from the race in which he said he was "just gutted" to have been removed from the race after coming back from severe leg injury last year.
"What can I say, just absolutely gutted," Rowe wrote of his disqualification.
"I don't know if the full footage was shown, but there was a big flick in the line and I was on the end of it. It was either crash of go onto the bike path.
"In a split-second decision I ended up on [the] bike path, braked and made my way back to the road when it was safe to do so.
"They told me on the radio and I pulled out straight away.
"After the s**t fight against myself the last six months to be back to this race I'm just gutted to exit this race like this. The commissaires made a decision which I can't agree with but I gotta live with this, accept it and move on. In a nutshell, I'm just gutted."
Prior to the incident, Rowe had been helping to chase down the day's 11-rider escape group, working for Team Sky leader Michal Kwiatkowski at the front of the peloton.
Niki Terpstra (Quick-Step Floors) eventually won the race from a solo attack.
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