The former New Zealand Cricket chairman succeeded India's Sharad Pawar at the ICC Annual Conference in Kuala Lumpur, where former South Africa wicket-keeper David Richardson was confirmed as the new ICC chief executive at the end of compatriot Haroon Lorgat's four-year term.
"I believe that the challenges ahead are no less daunting than those we have faced in the last two years if we are to maintain the vibrancy and viability of the three formats of the sport," Isaac said in a statement.
"I look forward to serving the game with honesty and integrity and to the best of my ability. I look forward to handing on the guardianship of the sport with the game enjoying even greater health," he added.
Isaac takes over at a time when the ICC is perceived as too susceptible to the financial might of the Indian cricket board.
The governing body's failure to mandate the use of the Decision Review System earlier this week is cited as yet another instance of its helplessness against the Indian board, which has been steadfast in its opposition to the technology.
In the annual conference, the ICC agreed to create the post of an ICC Chairman, who would call the shots, remove the role of ICC vice-president and make the president's role "ceremonial in nature with a term of only one year."
The ICC board will select a chairman in 2014 with a two-year term.