A slang meaning of zoo is a place or situation marked by "confusion or disorder," or sometimes "chaos and unrestrained behavior." The interaction between Jerry and Peter in the play is certainly confusing, and the behavior at the end could be classified as "unrestrained."
On some level, playwright Edward Albee is using the word zoo as an analogy for the confrontation between Peter and Jerry. Since Jerry announces to Peter that he has just come from a literal zoo, and that something had happened to him there, it's natural to assume to that the title refers to the traditional definition of zoo, as a zoological garden. Several critics, however, believe that Albee intends the slang definition; still others perceive it as having dual meaning, a non-risque double entendre. Therefore, there is no clear-cut consensus on the reason for the title.