The Brazilian, who has scored eight goals so far this campaign, was injured in Roar's 3-3 AFC Champions League (ACL) draw against South Korea's Suwon Samsung FC at Gold Coast Stadium last Wednesday.
The club confirmed on Monday the 29 year-old will have surgery later this week and will be assessed afterwards to determine his chances of returning this season.
With only five weeks remaining before the finals that prospect appears highly unlikely.
The news is a big hit for Roar, which is locked in an intense battle with Melbourne City to secure the sixth finals position.
Roar is five points behind City with a game in hand.
The speedy winger, nicknamed 'Slippery Fish', was substituted in the 65th minute last Wednesday after earlier taking several heavy tackles.
Henrique was sidelined from Sunday night's 2-1 loss to A-League leader Wellington Phoenix - a match that was abandoned in the 73rd minute after heavy rain partially flooded the Suncorp Stadium field.
The Brazilian, who has been with Brisbane since 2009, said days earlier he was having his best season yet with the club.
The likes of Dimitri Petratos, who started on the left wing on Sunday, and Serbia international Andrija Kaluderovic, who scored Brisbane's lone goal, will now be among those considered to cover in Henrique's absence.
