Intonation and the changing of meaning

Two questions with the same words can have somewhat different meanings. For example, I could ask

1. Do you want to go to the zoo or the museum?

   with my intonation/pitch rising after zoo, or

2. Do you want to go to the zoo or the museum?

   with a higher intonation on zoo going down to a lower pitch by museum.

So, using only intonation, it seems we can distinguish between "here are two of our options" (1) and "here are our only two options" (2).

Is there a name for intonation changing the meaning of a sentence?

The ways in which the voice can convey meaning by means other than vocabulary and syntax are known collectively as prosody. I know of no single word for the particular feature you describe. However, changes in intonation can be described by terms such as low fall, mid fall, high rise, fall-rise and so on.

It seems that in your first sentence the change in pitch might be a low rise, and in the second a rise-fall. It is, however, impossible to be sure from the text alone. It would be necessary to hear a recording of the speech, and to analyse it as a whole. Previous speeches in the conversation, the relationship between the participants and the accompanying facial expressions would also be relevant.