Hughes, who was overlooked for the original squad despite scoring two half centuries against South Africa in the recent triangular one-day series in Zimbabwe, had been included in the Test squad to play Pakistan in the United Arab Emirates.
The 25-year-old was already scheduled to travel to the UAE earlier than his Test team mates to spend time working on his batting against spin with the team's coaching consultant, Sri Lanka great Muttiah Muralitharan.
In and out of the team with depressing regularity in his Test career, Hughes only made the trip to Zimbabwe for the ODI series after an injury to Shane Watson.
The lefthander boasts a batting average of 37.31 in his 24 one-day internationals and will now have his chance to earn a place in the squad for next year's World Cup, which Australia are co-hosting with New Zealand.
Clarke, Australia's leading batsman, flew home from Zimbabwe with an injury that "a series of investigations" confirmed to be a "significant hamstring injury", Cricket Australia physiotherapist Alex Kountouris said on Tuesday.
After a one-off Twenty20 match on Oct. 5, Australia play Pakistan in the three one-dayers before the first Test starts Oct. 22 in Dubai.
"We are hopeful that he will be available for the Test series but this will be determined at a date closer to the first Test," Kountouris added.