Trailing 3-0 in the finals after a disastrous away first leg in Malaysia, Indonesia were handed the perfect platform at home to get back into the tie when they were awarded a 19th minute penalty.
Firman Utina's weak spot kick was however saved by Malaysian stopper Khairul. Rajagobal's men duly scored on the counter-attack in the 54th minute to effectively kill any hopes of an Indonesian fightback.
Indonesia had to score five goals in the final 36 minutes to win - they could only score twice - but Rajagobal claims Malaysia had the right game plan in place even if the hosts had converted that first half penalty.
"Even if the penalty had gone in, I would not have done things very differently. I would have told the players to be more alert and to continue to try to get a goal," Rajagobal was quoted on the competition's official website as saying.
He added: "I knew that Indonesia would come out aggressively at the start so we had to try to remain focused and continue to play as a team and as a unit.
"We were a bit fortunate with the penalty save but at the end of the first half I felt that we were in a good position and so we continued to play the way we had been playing while trying to get a goal on the counter attack.
"Then we got a beautiful goal by Safee off a wonderful pass by Ashari and that made things harder for them and a little bit easier for us to win the AFF Suzuki Cup."
Malaysia won the tie 4-2 on aggregate to lift ASEAN's biggest football tournament for the first time in their history.