The Giver knew Jonas was leaving; he helped to develop the plan for the departure.
Jonas had come to the conclusion that there had to be a better way of living, and that the people of the community needed to share in the memories and the understandings only made possible by remembering the past. The Giver, having watched Jonas's thoughts and reactions and having talked with Jonas about the choices the community had made and the results of those choices, agrees that this radical change in the community's level of awareness is necessary.
Together, they create the plan that will allow Jonas's departure to go undetected for a long enough period of time to permit him to put a significant distance between himself and the community before the search for him begins. Jonas is forced to leave sooner than they had planned in order to save Gabe from being released.
Jonas never formally said "Good bye" to the Giver, but the Giver knew and supported Jonas's plan.