He posted a 2-under 70 to finish 54 holes at 11-under-par 205 and owns a one-shot lead over defending champion Nick Dougherty, who carded a 5-under 67 on Saturday.
Ross Fisher shot a 4-under 68 and Malaysian Open champion Charlie Wi fired a 7-under 65 to share third place at minus-9. Chapchai Nirat fashioned a 6-under 66 on Saturday and has sole possession of fifth place at eight- under-par 208.
With the final threesome on the final hole at the Masters Course at Laguna National Golf & Country Club, a thunder and lightning storm hit. It stopped play for almost two hours and the leader dropped a shot after the long stoppage.
Mamat began the third round with a one-shot lead, but quickly extended the margin with a birdie at the first. Prayad Marksaeng got one back with a birdie at No. 3, but Mamat once again claimed a two-shot edge with a birdie at the par-4 sixth.
Mamat, a former winner on the Asian Tour, which is co-sanctioning this event with the European Tour, birdied the par-4 ninth to make the turn with a three-shot cushion.
Marksaeng closed the gap with a birdie at ten, but double bogeyed the 11th to fall down the leaderboard. Charlie Wi was in the clubhouse at 9 under par and Dougherty got to the same score with a birdie at the 11th.
The defending champion reached minus-10 with a birdie at 14, but Mamat birdied the 15th to get to 13 under par. Mamat bogeyed the par-3 17th for the first time all week to see his lead shrink to two.
Mamat missed the fairway at the closing hole, then missed the putting surface with his second.
That's when the lightning storm hit.
Mamat could not save par after the hiatus and his lead fell to one.
If he can hold on, it would be Mamat's first victory on the European Tour. He won on the Asian Tour at the Royal Challenge Indian Open in March of 2004, but will have to ward off the man who is seventh on the current European Tour Order of Merit.
Dougherty flew out of the gate on Saturday when his 9-iron approach at the first stopped 6 feet from the hole. He rolled that birdie putt in, then got up and down for birdie at the par-5 second. Dougherty capped off three birdies in a row with a 15-footer at the third.
Things came undone for the defending champion when he double bogeyed the fourth hole, but Dougherty rebounded. He drained an 8-footer for birdie at the sixth, tapped in for birdie at the seventh and hit a 6-iron to four feet to set up his third birdie in a row at No. 8.
He bogeyed 10, but a pair of 4-foot birdie putts at 11 and 14 put him one behind.
'All I can do tomorrow is put pressure on him,' acknowledged Dougherty, who could become the first player to successfully defend his title at this event. 'The only way I'm going to do that is by hitting iron shots close.'
Anders Hansen and Andrew Butterfield both posted rounds of 6-under 66 and are knotted in sixth place at minus-7. Marksaeng, who shared second place at the start of the third round, struggled to a 2-over 74 on Saturday and is tied for eighth with Wade Ormsby, who managed an even-par 72 in the third round. The pair is knotted at 6-under-par 210.
Marcus Both, who shared second with Marksaeng after Friday's round, played poorly en route to a 5-over 77. He is part of a group tied for 22nd place at 3-under-par 213.