Injury-prone Watson will be replaced by New South Wales batsman Phillip Hughes who recently became the first Australian player to score a List A double hundred.
"His ankle is currently swollen and sore, but expected to recover with a period of rest," Australian team physiotherapist Alex Kountouris said in a statement about Watson's injury.
The decision was made to replace Watson as he is doubtful to recuperate in time for the triangular series.
"Due to the compact nature of the tour, we've made a decision that Shane would be unlikely to recover sufficiently in time for the series."
However the Australian team management is optimistic to have his services available for the important tour against Pakistan at UAE in October later this year.
© Cricket World 2014