Henderson suffered an early setback before Liverpool took the lead in their Champions League last-16 showdown at Bayern, as he hobbled off through injury.
Henderson appeared to land awkwardly after an aerial challenge with James Rodriguez and received treatment to his left ankle.
Although the England international tried to continue he was forced to make way for Fabinho during the 13th minute.
Jurgen Klopp's decision to start with Henderson, Georginio Wijnaldum and James Milner ahead of Fabinho raised eyebrows before kick-off at the Allianz Arena.
However, Sadio Mane put Liverpool 1-0 ahead on the night - as well as on aggregate - with a superb 26th-minute finish.
After Bayern equalised, Virgil van Dijk put Liverpool ahead before Mane scored his second of the night to round off a fantastic evening for the Reds in Munich.
But the win appears to have come at a cost.
"It's a big night with a little shadow that is Hendo's twisted ankle," Klopp said in his post-game press conference.
"We have to see. It looks serious enough, and when you have to change in the middle of the park it’s not ideal.
"That's always a bad sign for a game, when you have to change early. We trained with him there in that position - we wanted to, not to rest Fabinho, but we wanted to bring in fresh legs and Hendo had fresh legs but unfortunately that didn't help with the ankle."
Klopp's men will now hope to go one better than last year's Champions League campaign, where they battled through to the final before going down to Real Madrid.
Liverpool are also in the thick of the Premier League title race, trailing first-place Man City by just a point.