Irsay posted the news on his Twitter account, saying Manning will receive $69 million over the first three years of the deal and $90 million in total, adding that it is "salary cap-friendly."
The Colts have been trying to complete a long-term deal with the veteran signal-caller since putting the "franchise tag" on him before the NFL lockout.
Manning, however, has encountered health problems with an injured neck since then.
The Colts Friday indicated Manning was expected to miss the start of training camp while recovering, saying he "continues to progress, but there is no timetable for his return to unrestricted activity."