The 18-year-old has made a name for himself at Anfield this season, having been given the opportunity to impress by Jurgen Klopp.
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Bajcetic was absent as the Reds lost 1-0 to Real Madrid on Wednesday night, which confirmed their Champions League exit.
Klopp previously described the Spanish sensations injury as a 'stress response around the adductor', and the latest news comes as a huge blow for Liverpool as look to secure a place in the top four.
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Taking on Instagram, Bajcetic wrote: "Unfortunately I've picked up an injury that will keep me out until the end of the season.
"It's very sad to say goodbye to this amazing season for me but I understand this is part of football and will only make me stronger physically and mentally.
"I would also like to say thank you to you Reds for all the support through the season and I assure you I will do my best to be back stronger than ever."
The midfielder, who joined Liverpool from Celta Vigo at the age of 15, has been one of the positives for Klopp, given Liverpool's lacklustre campaign.
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Bajcetic previously earned praise from Mohamed Salah after Liverpool thrashed Bournemouth 9-0 at Anfield back in August.
The Egypt international told Sky Sports at the time: "He's a great player and person, he always tries to work hard. Since he started playing for us, he has been our best player maybe so hopefully he keeps that confidence and keeps going."
Since then, the highly-rated youngster netted his first goal for the Reds in a 3-1 victory over Aston Villa on Boxing Day, and also put in a man-of-the-match performance in the 7-0 victory over Manchester United.
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Liverpool will now have to try and make up ground for a place in the top four without their star, and will hope to have him back for the start of next season.