Left-hander Hughes made two double-centuries for Australia A in July/August - one in a 50-over match.
Hughes was also originally left out of Australia's squad for their tri-series tournament with South Africa and Zimbabwe, before getting a late call-up for the injured Shane Watson.
The New South Welshman went on to average over 40 in four ODIs in Zimbabwe, but was not named in the Australians' 14-man one-day squad for their tour with the Pakistanis in the United Arab Emirates.
Clarke's hamstring injury, though, has paved the way for another 11th-hour call-up for Hughes.
The ODI series begins in Dubai on October 7, after the two nations go head-to-head in a one-off Twenty20 international on October 5.
Hughes was already scheduled to visit the UAE as part of his Test match duties, with that two-game series starting on October 22.