Girmay became the first black African to win on any of cycling's three grand tours after claiming the honours on Tuesday's 10th stage of this year's race, between Pescara and Jesi.
Intermarche's team doctor Piet Daneels said tests showed "haemorrhage in the anterior chamber of the left eye".
"In consultation with the medical and sport staff, the decision has been made that Biniam Girmay will not take part any longer in this Giro d’Italia, which he is leaving with a stage victory, a second place and three other top five finishes," Intermarche said in a statement.
"The injury is moving in the right direction but in order not to aggravate it it has been strongly advised to avoid intense activities."
The cyclist had placed the bottle on the floor and bent over it as he undid the binding before the cork flew off hitting him from close range.
Girmay was treated at a hospital in Jesi before then heading to a party held by his team in the seaside resort of Riccione on Tuesday evening.
He is due to have further tests on the eye and left the team hotel on Wednesday morning with his manager after bidding farewell to his teammates
'LITTLE PIECE OF HISTORY'
Girmay has carved out a name for himself in the world of cycling, establishing himself as one of the sport's best sprinters.
He had already made history this season when he became the first African winner of a classic, the Ghent-Wevelgem at the end of March.
He shot to attention at the world championships when he became the first black African man to feature on the podium when he came second in the under-23's at the 2021 event in Belgium.
He has already racked up eight wins since turning professional in 2020.
On Tuesday the 22-year-old had proven too strong for Dutch ace Mathieu van der Poel, who threw up his hands in resignation after a long struggle for the line at Jesi.
While multiple tour winner Chris Froome was born in Kenya and Daryl Impey of South Africa has won stages, Girmay is the first Black African to win on the grand tours.
"I watched the Giro as a kid on television and then went out riding with the dream of one day taking part," Girmay said, before his podium accident.
"We write a little piece of history every day," he added.
"I'm really happy about what I did today, I don't have the words to describe it."
Impey paid tribute to Girmay's achievement in a post on Twitter: "What. A. Sprint. @GrmayeBiniam bossed that @giroditalia. Amazing for Eritrea and Africa again. He's just getting started, it seems. Chapeau (Hats off)!"
Girmay leaves the Giro second in the sprint points race, just three points behind Frenchman Arnaud Demare on 151, with Van der Poel third another 58pts behind.