The 31-year-old hobbled from the field in the first half and attempted to return in the second half only to have his left knee collapse on him without contact.
Back-up hooker Jayden Hodges is expected fill the dummy-half role for the side's final two matches.
The Sea Eagles must win their remaining games against the Sydney Roosters and Cronulla - and hope Canterbury and St George-Illawarra falter above them - to sneak into the finals.
Ballin confirmed earlier this year that he was one of several Sea Eagles told to look elsewhere for next season.
However, having penned a two-year extension with the club in April, the veteran rake declared he would fight to keep his spot in the team.
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