The club has been fined $750,000 and two officials - chief operating officer Neil Bare and former CEO Joe Kelly, who is now the boss at the Sydney Roosters - receiving 12-month bans.
Manly will also have a $660,000 penalty applied to their salary cap for this season and the 2019 Telstra Premiership.
The breaches involve 13 players over five years, totalling $1.5 million.
Sea Eagles coach Trent Barrett was given an official warning while club legend Bob Fulton, who did not make himself available during the investigation, would have to get NRL approval to return to any official role within the game.
Fulton, one of the eight Immortals, completed his term as a national selector after last year's World Cup and no longer holds any formal position at Manly after resigning as general manager of football last year.
NRL CEO Todd Greenberg said an investigation by the integrity unit had uncovered evidence of deliberate breaches of the cap.
"The investigation found a number of cases where players were offered undisclosed benefits outside the salary cap to attract them to the club," Greenberg said.
"These benefits were in the form of third-party agreements which were never declared to the salary cap auditor.
"In other words, Manly had a financial advantage in securing the services of players who may otherwise have gone to other clubs.
"Our salary cap is the main reason we have the closest competition in Australian sport and we will not tolerate any attempt to breach it.
"Every club needs to be aware that any attempt to cheat the salary cap will eventually be detected and the club involved will be heavily sanctioned."
At the press conference to announce the verdict, Greenberg said Manly had an advantage which was "grossly unfair to other clubs".
"One of our concerns from this investigation is that the club had every opportunity to come clean about the activities and to cooperate fully with the investigation. It did neither," he said.
"Yet the evidence obtained by the integrity unit is indeed compelling. The other clubs have every right to be angry, not just that the game's image has been tarnished by another salary cap saga, but because they may have missed the opportunity to sign players because of Manly's undisclosed deals.
"Fans have every right to be angry. This investigation again shows that if clubs breach the salary cap they will be caught."
Manly invited the NRL to conduct a salary cap review in July 2017.
The ensuing investigation reviewed more than 800,000 documents, emails and text messages and other data from the phones and computers of club officials.
Numerous current and former officials and players were interviewed. There were no findings of wrongdoing by the providers of third-party agreements to the Sea Eagles players.
The NRL has imposed the following penalties:
- A fine of $750,000 with $250,000 suspended if the club undertakes appropriate governance changes to ensure there is no repeat of the breaches;
- A $660,000 penalty to be applied to the club's salary cap. This will affect the club's salary cap this year and next year;
- Bare has had his registration suspended for 12 months but will be eligible to return to the game on January 1, 2019 if he undertakes appropriate governance training;
- Sydney Roosters CEO Joe Kelly, who was previously employed at Manly, has had his registration suspended for 12 months but will be eligible to return to the game on January 1, 2019 if he undertakes appropriate governance training.
This investigation again shows that if clubs breach the salary cap they will be caught.
Greenberg said Manly were now cap compliant and no competition points would be deducted.
"We have to ensure the penalties for cheating the cap remain a deterrent," he said.
"We have had such a successful start to the 2018 season that every fan from every club can reasonably expect their team to play in the finals.
"So we make no apology for taking a hard stance against breaches of the cap – it is something we will continue to be vigilant in protecting."
Manly and the officials can appeal the sanctions to the NRL Appeals Committee.