The answer to this question can be found in Chapter 53, when Pi tires to launch his raft so that he can escape the boat and the increasingly perilous situation that exists with being trapped on a life boat with a hyena and a tiger. Having killed the orangutang and the zebra, the hyena has kept a low profile due to its fear of the tiger. However, just as Pi is about to tie the knot that will secure the raft and enable him to float on it away from the boat, the tiger kills the hyena. Note how the text describes this event:
The flame-coloured carnivore emerged from beneath the tarpaulin and made for the hyena. The hyena was leaning against the stern bench, behind the zebra's carcass, transfixed. It did not put up a fight. Instead it shrank to the floor, lifting a forepaw in a futile gesture of defence. The look on its face was of terror. A massive paw landed on its shoulders. Richard Parker's jaws closed on the side of the hyenea's neck. Its glazed eyes widened. There was a noise of organic crunching as windpipe and spinal cord were crushed. The hyena shook. Its eyes went dull. It was over.
Thus it is that the hyena met its end at the hand, or rather paw, or Richard Parker, the tiger that now shares its precarious existence with Pi who is left with him alone.