The company said Bowen would receive his unused leave and long service entitlements, as well as a payment of $A384,773 in lieu of three-and-a-half months notice.
Bowen earned a total $3 million in 2011 and $2.8 million in 2012.
No future short-term incentives are payable to Bowen and his outstanding performance rights had already been cancelled.
Macmahon agreed to release Bowen from the clause in his contract which restricted him from dealing with customers and competitors of the company.
A deed of release has been signed and Bowen will have no ongoing role with Macmahon, despite initially planning to stay on as an advisor.
Bowen was replaced by chief operating officer Ross Carroll in September after lowering Macmahon’s full-year profit after tax to $20-40 million, after a record profit of $56.1 million last year.
Since then, all directors and senior executives have agreed to take a 10% pay cut.
Carroll’s base salary of $990,000, which includes the 10% cut, is 19.2% lower than Bowen’s.
However, Carroll can earn as much as $2.2 million this year if he meets all performance targets.