Normally the difference is made clear by context. Absent additional context, either could be correct; it all depends on her current state of vigor, and ultimately what one intends to say. However, the most common case would arguably be that both sentences refer to the same point in time. Consequently, since the first sentence is in past tense, the second sentence should also be in past tense.
As pointed out in the comments, both are linguistically correct, but they have different meaning in terms of the point in time at which the tiredness is/was current.
She walked for two hours. She must be tired.
This implies that the two-hour walk ended recently, by the first sentence being written in past tense and also by stating that she is likely to currently be tired. Since it is "walked" in past tense, the two hour walk has clearly ended; she may or may not have reached her destination, but she is not currently walking (that would have made the first sentence something like "she has been walking for two hours", in present tense, at which point having the second sentence in past tense would be confusing).
She walked for two hours. She must have been tired.
This implies that the two-hour walk has ended at an unspecified, earlier point in time, same as above. It also implies that at that time (at the time when the walk ended) she likely was tired (which by implication was the reason for her to stop walking).
Take a somewhat more extreme example, by specifying a point in time for the walk, and by making the time at which she was/is tired explicit.
She walked for two hours a week ago. She must be tired now.
The two sentences may both be correct, but they are pretty obviously unrelated (the fact that she walked for a few hours a week ago is unlikely to cause her to be tired now).
She walked for two hours a week ago. She must have been tired then.
This is clearly talking about her state of vigor at the time of her walk. It's not unreasonable to be tired after a two hour walk, so the second sentence follows reasonably naturally from the first.