Trailing 3-0 from the first leg, Indonesia squandered an opportunity to cut the deficit when Firman Utina's weak spot kick in the 15th minute was stopped by Khairul. And the home team's hopes of rescuing the match were effectively snuffed out when Safee scored on the break nine minutes into the second half.
Mohammad Nasuha pulled back a goal with 18 minutes remaining and Muhammad Nasuha scored with a deflected effort two minutes from time to give the home side the win on the night although Malaysia still prevailed 4-2 on aggregate.
The Malaysians had lost their opening match of the tournament 5-1 to the Indonesians but they claimed the AFF Suzuki Cup by allowing only three goals in their last five games. Meanwhile, the Indonesians were left to rue yet another disappointing end to an AFF Suzuki Cup campaign as they lost in the final for a fourth time.
Both sides made two changes to their starting line-ups from the first leg. Arif Suyono replaced the suspended Oktovianus Maniani on the left of Indonesia's midfield while striker Irfan Bachdim was brought back in to replace Yongki Aribowo, who was ruled out with a knee injury.
For Malaysia, right-back Sabre Abu and right midfielder Ashari Samsuddin came in for the suspended Mahalli Jasuli and Amirulhadi Zainal.
The crowd, which included Indonesian president Susilo Bambang Yudhoyono, had filled every seat in the 85,000-capacity stadium nearly two hours before kick-off, hoping to roar their team on to the quick start that they needed to turn the tie around after their decisive loss in the first leg.
The home side's first real opportunity arrived in the 17th minute when a long free-kick by Zulkifli Syukur was flicked on by Cristain Gonzales to his strike partner Irfan Bachdim, who stabbed his effort from close range straight at the goalkeeper.
The Indonesians were presented with a gilt-edged opportunity to take the lead two minutes later when Australian referee Peter Green awarded pointed to the penalty spot after spotting a handball by a Malaysian defender as several players went up for a high ball into the box.
Skipper Firman took responsibility for the penalty but his weak effort was easily saved by Khairul, who dived low to his left.
The Malaysians were a constant menace on the counter-attack and they nearly got the crucial away goal a minute later when Ashari Samsuddin received a pass from Norshahrul Idlan and went past the challenge of Hamka Hamzah before unleashing a fierce low drive that goalkeeper Markus Harison did well to parry.
On 25 minutes, a cross from the right by-line by Ridwan took a deflection off Malaysian defender Asraruddin Putra and looped up to the far post to Gonzales, who failed to put his header on target.
A minute later, a free-kick by Firman found Ridwan and Gonzales unmarked at the far post, but the pair appeared to get in each other's way and Gonzales headed over.
Two minutes before the break, the ball dropped to Gonzales on the left of the box but his effort from a narrow angle flew well over the crossbar.
And right before half-time, the Malaysians had to resort to some desperate defending to keep out an effort by Ridwan before Muslim Ahmad headed out a goal-bound effort from under his crossbar.
The Indonesians continued to force the issue after the break but despite dominating play, they were caught on the break in the 54th minute after giving away possession cheaply just inside their own half.
Norshahrul launched the ball forward to Safee, who outpaced the Indonesian defence before lashing the ball into the top left corner of the net for his tournament-leading fifth goal.
Needing five goals now to win the tie, Indonesia coach Alfred Riedl threw on Bambang Pamungkas and Eka Ramdani to replace Irfan and Firman.
The Malaysian continued to hold firm but their run of three clean sheets was finally ended in the 72nd minute when Khairul could only parry a shot by Bambang, which allowed Nasuha to put away the rebound, giving the home fans some renewed hope.
The Indonesian continued to press but could not manage another breakthrough until the 88th minute when Ridwan's shot from the edge of the box took a deflection off a Malaysian defender on its way past Khairul.
Bambang had a chance to net a third for the Indonesians in stoppage time but his free-kick was well saved by Khairul as the Malaysians easily hung on to claim the title.
AFF SUZUKI CUP 2010
Most Valuable Player : Firman Utina (Indonesia)
Top Scorer : Mohd Safee bin Mohd Sali (Malaysia - 5 goal)
Fair Play Award : Philippines
Winner : US$100 ribu (Malaysia)
Total Tournament : 51 goals, 65 yellow cards, 4 red cards
Indonesia's Irfan and Malaysia's Safiq fight for ball during final match of
AFF Suzuki Cup 2010 soccer tournament in Jakarta
AFF Suzuki Cup 2010 soccer tournament in Jakarta
All Picture, AFF Suzuki Cup Final 2010