The matches will be played on August 28 in Sharjah, August 31 in Abu Dhabi and again in Sharjah on September 3.
The teams will also play three Twenty20s, for which a team was announced last month.
Khan, 34, had been a lean form during a five-match away one-day series against Sri Lanka last month, scoring only 10 runs in four innings.
He has so far played 245 one-days for Pakistan, scoring 6,824 runs, but his last hundred came four years ago. Also out of the squad is ace paceman Umar Gul, who managed just four wickets in four matches against Sri Lanka.
Chief selector Iqbal Qasim said both Younis and Gul, a 28-year-old veteran of 111 one-day matches, have been rested.
"If you look at the last series against Sri Lanka, both Younis and Gul were struggling with form so we have rested them for the two tough series ahead, the first against India in December and then against South Africa early next year," Qasim told AFP.
Qasim denied Younis's career was over.
"By no means (is it) over, he can stage a comeback after rest," said Qasim.
Wicket-keeper batsman Kamran Akmal, already recalled for the Twenty20 series against Australia, also bagged a place in the one-day team.
"We observed during the Sri Lanka series that our batting struggled, especially the lower order, so we included Kamran who gives solidity to the batting," said Qasim.
Opener Nasir Jamshed, withdrawn from the team for Sri Lanka due to a finger injury, will also make a return, as will all-rounder Anwar Ali.
Ali, 23, has played just one Twenty20 for Pakistan, in 2008.
The three Twenty20s against Australia will be played on September 5, 7 and 10 - all in Dubai.
Squad: Misbahul Haq (captain), Nasir Jamshed, Mohammad Hafeez, Azhar Ali, Asad Shafiq, Umar Akmal, Kamran Akmal, Shahid Afridi, Sohail Tanveer, Aizaz Cheema, Saeed Ajmal, Imran Farhat, Shoaib Malik, Abdur Rehman, Junaid Khan, Anwar Ali
COMMENTS (10)
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where is Abdul Razzaq?
if u want to give shoaib malik a chance then play him at 1 or 2 down so that he has enough time at the crease to show that he is well and truly in form
Good team and balanced selection. YK is not performing in limited overs cricket at all. He should be part of the test squad only. Gul was totally off color against Sri Lankans so all in all a good team selection
I think this is a good move! Younis time is up. He did well but its time to move on for Pakistan cricket and him. Also, Gul was in team mostly because of loss of Aamir and Asif. He is a hardworking peron but an average bowler who gets beating quite often from every one. It is time to try others.
Selection of Kamran Akmal, Shoaib Malik and Imran Farhat is a joke.
The headline is kind of harsh towards Younis Khan, and what happened to the fact that he batted wonderfully in the tests and showed that he was back in form?
Kamran Akmal is back. Board officials will get rich. Pakistan will lose.
@Truth Detector: When Kamran Akmal is in the team then any thing is possible.
and you will have to defy the immutable laws of physics or invent time-machine to watch the game on August 8th...Wake up, ET...