McKinnon -- whose title was group executive, technology services -- leaves early in the tenure of the CBA's new chief executive, Ralph Norris, who "expressed regret" at the move.
In a statement, Norris said McKinnon had been "an important member of the bank's senior executive team, having been responsible for the technology services division at a time of important change.
"Whilst it is always disappointing to lose a senior executive, I can understand that there are opportunities that one must take and I wish Bob well in his new role".
The CBA said a search process would be conducted between now and the end of the year for a replacement for McKinnon.
