Rixon will be Acting Head Coach for the ODI against Afghanistan, as well as the three ODIs against Pakistan. Mickey Arthur will return to see the third ODI against Pakistan and resume as head coach for the T20 series, a CA media release said.
The plan is part of the Australian Team Performance Review recommendations and the revised broader role the Head Coach has.
In his couple of weeks away from the Australian team, Arthur will use the time to prepare plans for the Australian T20 team ahead of the series against Pakistan and for the ICC World Twenty20, working on team tactics, strategies and opposition analysis.
"Part of the broader scope of the new Australian team Head Coach role since the ATPR was conducted was to have a wider view over the team's plans and how we prepare and we have a very important T20 tournament coming up," Arthur said.
"I'll spend the time away from the team to really hone our T20 plans and study the opposition ahead of the ICC World Twenty20.
"We have great experience and harmony within our support staff group now and I know that Steve will do a terrific job in partnership with Justin Langer and Ali de Winter while I'm away".
Rixon said that while he was looking forward to the opportunity, that his job was to simply carry on the good plans in place.
"Of course you look forward to opportunities like this; it's not every day you get to coach the Australian Cricket Team and I'm looking forward to that extra responsibility and working with Michael Clarke," Rixon said.
"In saying that, my job will be to simply carry on with all the good work and planning that has been done in recent times and hopefully hand back over to Mickey after four good wins."
While coach, Rixon will act as a selector as Arthur normally would.
Meanwhile, the Australian ODI squad will depart for the UAE on Tuesday.