Schwartzel, who won back-to-back tournaments in December last year by a combined total of 23 shots, was four under par after 11 holes of his first round when thunderstorms forced play to be abandoned for the day on Thursday.
The South African was among 78 players who resumed play this morning at 7:45am local time and completed an opening 67 in style, chipping in for a birdie on the 18th.
That left the 2011 US Masters champion two shots off the clubhouse lead held by Thailand's Kiradech Aphibarnrat, but it did not take him long to wipe out that deficit when the second round got under way.
Starting from the 10th, Schwartzel birdied his first two holes and picked up two more shots on the 17th and 18th to be out in 32, while further birdies followed on the third and fifth.
At that stage he enjoyed a three-shot lead and looked capable of another runaway victory, but bogeys at the sixth and seventh meant he had to settle for a 68 and nine-under-par halfway total of 135.
China's Ashun Wu was also safely in the clubhouse on nine under after five birdies and one bogey in his 68, while Scotland's Alastair Forsyth - winner of the event in 2002 - was two behind with two holes of his second round to play.
World number three Luke Donald, who needed a major improvement on his opening 74 to make the cut, had just started his round when play was suspended.
Tournament officials had been hoping for an early finish on Sunday to allow the Malaysian prime minister to attend the prize-giving ceremony before going on to the Formula 1 Grand Prix at nearby Sepang.
Play eventually resumed after a delay of around two and a half hours, but with only around an hour of daylight left, half the field would be returning early tomorrow to complete their rounds.
Schwartzel, who played 25 holes in the sweltering heat which contributed to playing partner Chris Wood withdrawing through illness, said: "I think the afternoon boys won't finish today [Friday] and it will be their turn tomorrow [Saturday].
"I suppose I can't be too hard on myself. It's really extraordinarily hot out there and it was a bit of lack of concentration on the end. I made a bad decision on six with club selection and then hit a very poor shot on seven.
"It was a long day out there but overall I feel I played pretty well and am at least giving myself a chance.
"I am playing consistently. If I was a bit sharper I could have really separated myself, but the game is good and shows me if I keep doing that hopefully by Sunday, or whenever we finish, I will be on top."