Healing factors have their limits. Wolverine's was weakened for a long time because it kept the adamantium in his body from poisoning him to death. X-23 has a better healing factor since she doesn't have as much adamantium, and she still nearly died when Nimrod -- a future version of the robots specifically designed to kill mutants -- blasted her. Makes sense that a master poisoner like Viper could cook up something deadly enough to threaten Sabertooth's life.