James Faulkner has been ruled out of Australia's Test tour of South Africa due to a knee injury and Shaun Marsh and Jackson Bird are still in doubt and will remain in Australia for further assessment while the rest of the squad departs on Wednesday.

Faulkner has been replaced in the squad by fellow allrounder Moises Henriques, who played his only three Tests on the tour of India early last year and will fly to South Africa after playing in Wednesday's first Twenty20 against England in Hobart. Faulkner will have arthroscopic surgery on his right knee on Tuesday after picking up an injury during Sunday's final one-day international against England in Adelaide.

"James' exact rehab plan and return to training and playing will be determined after surgery but unfortunately for him, he will not be available for the upcoming Test tour of South Africa," the team physio Alex Kountouris said. "We are hopeful that he will recover in time to play the Twenty 20 games on that tour and take part in the ICC World Twenty20."

Faulkner's presence in the Test squad would have given the selectors another option for balancing the side in South Africa if they chose to move the wicketkeeper Brad Haddin up to No.6. Henriques appears much less likely to play in the Tests than Faulkner would have; Henriques played three Sheffield Shield matches in the first half of the season and scored 202 runs at 33.66 and took five wickets at 36.60.

In the last Shield match before the break for the BBL, Henriques scored 127 against South Australia, and he said that innings helped him gain some momentum heading in to the Twenty20 tournament. The challenge of Test cricket in South Africa against an attack boasting the top two bowlers on the ICC's Test rankings will be immense, but Henriques believes his batting has improved in the past few seasons.

"I certainly feel like my batting has progressed over the last couple of years ... I feel like I'm learning quicker now," Henriques said. "It's going to be tough. It will be completely different conditions in South Africa so I'll have to learn on the go over there. Their bowling attack will be very different to the bowling attack that India threw at us in the Test series over there."

The Australians also have concerns over the fitness of Marsh, who strained his calf during the ODI victory in Adelaide. Marsh had been scheduled to travel to South Africa on Tuesday night but instead will remain in Perth for further treatment over the coming days and Cricket Australia said in a statement that "a decision on whether he will travel to South Africa will be made in due course".

Similar doubts will keep Bird in Australia while the rest of the squad departs. Bird jarred his back while fielding for the Melbourne Stars in a BBL match last week and Cricket Australia confirmed he will remain in Hobart "to be assessed by CA's medical staff and return to bowling to determine if he has recovered sufficiently enough to take his place on the South Africa tour".

Bird was unlikely to be in the starting XI for the first Test in Centurion, given the success of the pace trio of Mitchell Johnson, Ryan Harris and Peter Siddle during the Ashes. However, when the squad was named last week there appeared a strong chance that Marsh would be part of the starting XI, given the absence of the incumbent No.6 George Bailey from the squad.

The majority of Australia's Test players will depart for South Africa over the next two days, although their first official tour match does not begin until next Wednesday in Potchefstroom. Faulkner had been the only player from the Test squad also named for the T20s against England over the coming week; his place in the T20 squad will now be taken by the fast bowler Kane Richardson.