Henderson suffered a knee injury in Thursday's (AEST) 3-1 Premier League win over Brighton and Hove Albion, with Jurgen Klopp confirming on Saturday (AEST) that it will force the midfielder to miss the remainder of the season.
The Reds captain has featured 30 times for Liverpool in the competition, helping it to a maiden Premier League title and a first top-flight crown in 30 years.
Klopp is optimistic the England international will be fit in time for the start of the 2020-2021 season as he does not require surgery, and the player will now focus on his rehabilitation.
Nevertheless, the injury will not prevent Henderson from lifting the Premier League trophy later this month.
"Unfortunately, [after] the knee injury I picked up against Brighton on Wednesday, I will now miss the last two weeks of the season," he wrote on his official social media accounts.
"However, my rehabilitation will start immediately and I'll be working hard to be back to full fitness in just a matter of weeks in order to be fully ready for the start of the new season.
"Of course, it's not the way I'd have preferred to finish the season on a personal level, but it's been an incredible campaign for us so far as a team and as a club, and I'll be doing everything I can to support the boys for the final games from the sidelines. I'm sure the lads will ensure we finish the season off on a high.
"Thanks to everyone for the messages of support and I look forward to being back out there as soon as possible."
Henderson will miss matches against Burnley, Arsenal, Chelsea and Newcastle United, bitter rival of his boyhood club Sunderland, as Liverpool aims to reach a century of points.