Possible meanings are 1) they first woke Jesus and then they said, "Save us" or 2) as they were waking Jesus up, they were saying "Save us."
# us ... we
If you need to translate these words as inclusive or exclusive, then inclusive is best. The disciples probably meant they wanted Jesus to save the disciples and himself from drowning. (See: [[rc://en/ta/man/translate/figs-inclusive]])