Off-spinner Hauritz, who played in the last Ashes test in England last year and has taken 63 wickets in 17 tests, struggled on the recent tour of India and was only able to bowl one over in Sheffield Shield action this week.
Left-armer Doherty impressed with four wickets on his international debut in a one-day match against Sri Lanka two weeks ago, which Australia still contrived to lose from a dominant position.
"Nathan Hauritz is one of these players omitted and he can consider himself unlucky as his Australian record has been very good over the past 12 months," Andrew Hilditch, the chairman of selectors, said.
"However, the panel believes the left-arm orthodox variety Xavier Doherty provides against a predominantly right-handed English middle-order is the better option in this game."
Leg-spinning all-rounder Steve Smith was also retained in the 13-man squad for Thursday's first test although the 21-year-old is most likely to be in contention for the 12th man berth.
Harris's omission still leaves four fast bowlers -- Mitchell Johnson, Ben Hilfenhaus, Peter Siddle and Doug Bollinger -- in the squad although only three of them are likely to start the first test on what is likely to be a lively pitch at the Gabba.
"We felt Ryan Harris needed further time to recover from his knee injury and also believe the four fast bowlers we have selected are in good form and will be key weapons for us winning the Ashes series this summer," Hilditch added.
The dropping of Ferguson and Khawaja means a reprieve for 35-year-old Mike Hussey, who hit a century for Western Australia on Friday, and Marcus North.
"Callum and Usman are both wonderful young players who we believe will play a big role for Australian cricket moving forward but on this occasion the experienced middle-order has been preferred," Hilditch added.Johnson promises England a torrid time
Vice-captain Michael Clarke, who suffered the recurrence of a back problem last week, and opener Simon Katich (shoulder) are also retained in the squad, which will gather in Brisbane on Sunday.
England, who are defending the Ashes, will name their team on the first morning of the test on Thursday.
Squad: Ricky Ponting (captain), Michael Clarke, Doug Bollinger, Xavier Doherty, Brad Haddin, Mike Hussey, Ben Hilfenhaus, Mitchell Johnson, Simon Katich, Marcus North, Peter Siddle, Steve Smith, Shane Watson.