Haddin, who was flown in as replacement for the injured Matthew Wade, will be playing his first Test in more than a year. Haddin was part of the series in the West Indies in January last year but left the tour mid-way due to personal reasons.
Clarke will also reshuffle the batting order. He will be promoting himself from No 5 to No 3 and will be followed by Phil Hughes and Steve Smith, who has not played a Test since the Ashes in Sydney two years ago.
Hughes was almost certain to be replaced by Khawaja but after the discipline breach, the former has certainly saved his place for the time being.