The Chilean finished 54 holes at 16-under 194 and two shots in front of a pair of players at Cengkareng Golf Club.
Jeev Milkha Singh carded a 5-under 65 to join Liang Wen-Chong, who fired a 64 on Saturday, in a tie for second place. The pair is in at 14-under-par 196.
James Kamte and Prom Meesawat both shot rounds of 2-under 68 on Saturday to share fourth at minus-13.
Aguilar began Saturday's third round with a two-shot lead, but that was quickly erased thanks to a bogey at the first and a Kamte birdie at the second.
Aguilar stayed at 12-under for a good part of the opening nine and a few players joined him there. Meesawat and Martin Wiegele matched Aguilar in the lead, but Aguilar moved clear with a birdie at the seventh.
A 25-footer for eagle at the par-5 ninth put Aguilar two clear of the field as Wiegele stayed in the hunt. Wiegele plummeted down the leaderboard thanks to three bogeys and a double-bogey in his last six holes.
For Aguilar, that eagle might have been the most challenging putt of the tournament. On Friday, during his round of 62, he estimated he faced only three putts longer than 15 feet.
'I think that eagle putt is the longest putt I have had all week,' said Aguilar.
At the 11th, Aguilar recorded another birdie to reach 16-under par for the championship. He parred his remaining seven holes to take a two-shot lead into the final round.
Aguilar has never won on the European Tour, but did collect a pair of victories last season on the Challenge Tour. He has participated in only one European Tour event this year and missed the cut last week at the Indian Masters.
'It feels pretty good going into tomorrow, but you never know if you're going to win until the last putt drops,' said Aguilar. 'We'll find out tomorrow when the fat lady sings! We'll know after 18 holes tomorrow.
'I really hope it's me but you can never tell with this game. Nothing is for sure in this game.'
That is a sentiment echoed by his closest pursuers.
'I just want to go out there tomorrow and follow my processes and routines,' said Singh, a two-time winner in Europe who used four birdies in a five-hole span before the turn to surge up the leaderboard. 'If it comes to me then great, but we will see what happens.'
'I'm ready to mount a strong challenge tomorrow,' said Wen-chong, the 2007 Asian Tour Number One who posted a 29 on the back nine Saturday. 'I'll try my best. Anything can happen in this game so we are just going to have to wait and see what happens.'
Mark Brown (66), Joost Luiten (66), Prayad Marksaeng (69) and Ter-Chang Wang (66) share sixth place at 11-under-par 199.
Arjun Atwal (66), Adam Blyth (67), Philip Golding (65) and Wiegele (70) are knotted in 10th at minus-10.
Defending champion Mikko Ilonen struggled in Saturday's third round. He posted a 1-over 71 and fell into a large group tied for 37th place at 5-under- par 205.