The Japan international was subbed off just after nine minutes against Sporting last week in the Europa League.
He will have to undergo a knee surgery after the injury and will miss the rest of the season.
Mikel Arteta was waiting for further assessments of the injury and the defender finally underwent knee surgery on Tuesday in London.
Tomiyasu now joins Eddie Nketiah, William Saliba and Mohamed Elneny in the treatment room.
“Following his substitution during last Thursday’s Europa League match, subsequent assessments have confirmed that Takehiro Tomiyasu sustained a significant injury to his right knee,” Arsenal said in a statement.
“Tomi has had successful surgery in London on Tuesday and will be ruled out for the remainder of this season.”
The 24-year-old defender’s absence will pose a huge problem to Mikel Arteta who has been brilliant for the Gunners this campaign.
Although Tomiyasu has played second fiddle to Ben White in the right-back position, his absence would cause complications in the Arsenal lineup.
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