The tropical thunderstorms may have created havoc by reducing the tournament into a 54-hole contest but it was Garcia who showed he was still the one in control after winning his 24th professional victory with a winning total of 18-under-par 198.
American Jonathan Moore matched Garcia's superlative efforts by also closing with a 61 to secure his second runner-up finish this season while Thailand's Thongchai Jaidee signed for his week's best score of 65 to take third place at the Horizon Hills Golf and Country Club.
Overnight leader Daniel Chopra of Sweden had to settle for fourth place after a final 69.
Although Thailand's Thaworn Wiratchant signed off with a 65 to take a share of fifth place, the 45-year-old also ended up a winner as he lifted the Asian Tour Order of Merit title for the second time since 2005.
Garcia came into the week as the highest ranked player and will leave his mark by writing a slice of history at the Asian Tour season-ending event.
The Spaniard's closing 61 is the lowest final round by a winner in the Asian Tour history after he blitzed the course with seven birdies in his front-nine and a further four in his inward-nine.
However it will not be counted as an official record as the preferred lies rule was in play.
"It has been a long week obviously because of the weather and I couldn't have asked for a better way to end the week. It has been a great experience as this is my first time in Malaysia and to be able to win is a treat," said Garcia.
"The most important thing about playing under these kinds of conditions is to keep the momentum going especially with so much disruption. It's hard to keep up mentally and I sort of did that yesterday morning where I finished poorly. But today, I came back strongly.I played very solid in my front-nine and made four in a row in the back-nine to give myself a nice solid lead going into the last two holes," said Garcia.
It was also a day to remember for Moore who could not have scripted a better story with his 61 to end his season on a high.
Moore, who came through the Asian Development Tour as the number one player last year, started his spectacular run when he birdied two of his opening three holes.
He then parred his fourth hole before going on to reach the turn in 29 after carding further birdies on holes five, six, eight as well as an eagle-three on the ninth hole.
The American set the stage for an amazing finish when he stormed home with four more birdies on holes 12, 13, 15 and 16.
"It was a really special day. I had a clear focus today and felt good on the greens. It was probably the best I have ever done because I didn't have any fear over any shots. It is probably one of those things in my career that you don't doubt and worry where the ball might end up," said Moore.
"It has been a good season. I'm just so thankful. It is hard to put it into words but it is such a huge blossom. This is my best score. I've shot two 62s before and won! But this time, there's a guy named Sergio Garcia who also shot a 61. It was a lot of fun to do that today," added the American.
Widely regarded as the Asian Tour's most successful player with his unprecedented three Merit crowns, Thongchai kept pace with Garcia throughout the day with his flurry of birdies until the par-five 15th.
The Thai was let down by his putting after he failed to make more birdies to pile the pressure on Garcia.
"I hit most of the greens but it was only my putting which let me down. If I putted well, I would have a good chance of winning. I missed a lot of birdie putts on at least seven or eight holes," said Thongchai who marked his card with eight birdies against one bogey.
While Thongchai could not end the year with another victory following his first victory in Europe in June, he believes he will be back to contend again after taking a well-deserved break.
"My confidence is up. I just need to practise my putter. This is my eighth tournament and I'm looking forward to a good holiday," said Thongchai who leads the Career Earnings list with over US$4.5 million in winnings thanks largely to 13 Asian Tour victories.
The Iskandar Johor Open is presented by Iskandar Waterfront Holdings Sdn Bhd, which is a government-linked company specifically incorporated to take on the role of master developer of prime waterfront properties in Johor Bahru.
The leading Australian was Scott Barr who finished 15th, while Marcus Fraser, Unho Park and Rick Kulacz were 21st.
Leading final round scores
198 - Sergio GARCIA (ESP) 68-69-61
201 - Jonathan MOORE (USA) 69-71-61
202 - Thongchai JAIDEE (THA) 66-71-65
203 - Daniel CHOPRA (SWE) 68-66-69
205 - Thaworn WIRATCHANT (THA) 71-69-65, Masanori KOBAYASHI (JPN) 71-67-67, Angelo QUE (PHI) 67-70-68, Antonio LASCUNA (PHI) 68-68-69, Chapchai NIRAT (THA) 68-67-70
206 - Shiv KAPUR (IND) 67-70-69, S.S.P. CHOWRASIA (IND) 67-69-70