The Portuguese star's afternoon was brought to an abrupt end against the Bees when he went in for a challenge with Christian Norgaard.
After colliding in the air, Norgaard inadvertently fell onto the Liverpool star's leg, causing it to bend in a way that looked very painful.
After receiving treatment on the pitch, Jota tried to stand up but immediately crumpled back down to the turf before being stretchered off the pitch.
Jurgen Klopp couldn't believe what he was seeing as he watched on with his hands on his head.
Jota wasn't the only injury worry of the day either, with Curtis Jones going off with an ankle problem and Darwin Nunez being withdrawn at half-time.
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Discussing the injuries, Klopp said: "It's mixed emotions because we lost players, which we don't know how serious they are, but it doesn't look great for either of them.
"We are having bad luck."I think it was a knock to Curtis' leg and we will see on that. It was a challenge with Diogo.
"Darwin, we were not sure if he has something or not, so we decided at half time to bring Cody [Gakpo] on, which was a good idea."
With the Carabao Cup final clash with Chelsea coming up, Liverpool's lengthy injury list will certainly be a cause for concern.
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The Wembley clash will be Liverpool's first chance to secure silverware this term, with Klopp's side also targeting silverware elsewhere.
With the Reds competing in the Europa League and the FA Cup, Liverpool are also looking strong in the Premier League with their 4-1 victory over Brentford putting them clear at the top of the table.