Under reforms Manohar himself had initiated within the ICC as its former chief earlier this year, the chairman must be an independent candidate with no formal links to his home board.
Manohar, who resigned as the president of the powerful Indian cricket board (BCCI) on Tuesday, commenced his two-year term at ICC with immediate effect.
"It is an honour to be elected as the Chairman of the International Cricket Council and for that I am thankful to all the ICC directors who have put their faith and trust in my abilities," Manohar, 58, said in a statement.
"I also take this opportunity to thank all my colleagues in the BCCI who have supported me during my recent time as the BCCI's President."
During his previous ICC stint, Manohar was instrumental in overturning the constitutional changes made in 2014 that gave India, England and Australia almost total control of cricket's administration.
The ICC full council approved the constitutional amendments which will see the president's post abolished after the governing body's annual conference in Edinburgh.
A lawyer by profession, Manohar served as BCCI president from 2008-2011 and was re-elected to the powerful position in October 2015 after the death of Jagmohan Dalmiya.
As BCCI president, Manohar brought significant transparency into the functioning of a board traditionally perceived as an efficient but opaque body.
"These are exciting times for international cricket as we are presently carrying out a comprehensive review of the 2014 constitutional amendments which is aimed at not only improving governance structures, but cricket structures as well," he said.
"The ultimate objective is to grow our sport and engage a whole new generation of fans and I look forward to working with all stakeholders to shape the future of cricket, which has a proud history and rich tradition."
(Reporting by Sudipto Ganguly in Mumbai; editing by Amlan Chakraborty)
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