The appointment followed the resignation of Nikos Kardassis on June seven after he served two terms as CEO between 1993-1999 and again from October 2009 till May 2013.
Toomey, 58, an Australian national, has previously served as President and CEO of the Air New Zealand Group and CEO of Airlines PNG in Papua New Guinea during periods of their major expansion.
Before this, he had served in various positions in Australian carrier Qantas, including as a Director, Deputy CEO and Chief Financial Officer.
A Jet spokesperson said Ali would continue as Acting CEO till Toomey's appointment received regulatory approval.
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In a statement, Jet chief Naresh Goyal said Kardassis had "made a significant contribution to Jet Airways, particularly in the development of our international network, laying the foundation for our future expansion."
He said Toomey has "extensive experience in domestic and international airline management, and the right credentials and skills to take Jet Airways forward."
Toomey, on his part, said the fast-growing Indian aviation market "offered significant potential for Jet Airways not only within India, but beyond, through new or improved international connections. I am delighted to have been selected to lead the Company and continue the development and growth of Jet Airways."