I am also stuck on this part, i think when he is on the ground, he get's up to regenerate himself, while he is doing that stand behind him and kill him with the syringe, by pressing triangle. Then you end the fight and you go onto fighting large geko's!
Stand behind him and press R1 as he is in the process of getting back up, make sure you have the syringe active in your inventory slot, and when you grab him, you press Triangle to stick him in the neck.
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