The ex-Yorkshire and Sussex head coach has signed a two-year deal and will start his tenure as Test coach for England's tour of Pakistan later this year.
Former South Africa player and coach Gary Kirsten will take charge of Pakistan's white-ball sides while ex-Pakistan all-rounder Azhar Mahmood has been named assistant across all formats.
"Leading the Pakistan cricket team is a big achievement for any coach, given its rich legacy and passionate fan base," Gillespie said in a statement.
"I love Test cricket and being able to focus on that is something I like very much. I also love the fact that there is so much talent in Pakistan.
"I understand there will be expectation and that comes with the role. All I can do is to take it in my stride and I would not have taken on the job if I did not think I could deal with it."
Gillespie resigned from his role as South Australia and Adelaide Strikers men's head coach last month.
That came after another disappointing season when the Redbacks finished in the bottom half of the Sheffield Shield table for the fourth time in his four years at the helm.
Gillespie will take charge of Pakistan's red-ball team in August when they play home matches for the World Test Championship against Bangladesh.
The series will be followed by test matches against England in October before the team tours South Africa for WTC matches in December.
Kirsten, who coached India to World Cup glory in 2011, added: "It's a tremendous honour to be entrusted with the responsibility of coaching the Pakistan men's national team in white-ball cricket and to rejoin the international cricket arena after some time. I eagerly anticipate this opportunity and aim to contribute positively to the Pakistan men's national team in limited-overs cricket."
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