The tournament in Vilamoura had already been reduced to 54 holes on Friday, with the majority of players left to finish their second rounds a day late.
And the field was forced to contend with more challenging weather conditions on Saturday - with Aguilar in particular seeing his momentum halted.
The Chilean, who started on hole 10, began brightly and was five under for the day after completing his front nine.
A further three birdies saw him close to within four shots of runaway leader Alexander Levy by the time the weather delayed his round after 14 holes.
Levy, who was one of the few to finish his round on Friday, might have been concerned for his 18-under-par lead, but a bogey on hole seven saw Aguilar fall a shot further back.
Aguilar now sits third on 13 under heading into the final day, while second-placed Nicolas Colsaerts, who hit a sublime 60 on day one, was unable to close the gap on Levy after losing top spot to the Frenchman on Friday.
The big-hitting Belgian had just two holes to reduce the three-shot deficit on Saturday, but hit pars at the eighth and ninth to post a 67 for his second round.
"It's always difficult to follow a really low score, but I'm quite happy with the way I played on the back nine coming in,” said Colsaerts. "I got to the golf course yesterday at 7am and left at 7.30pm, so it was a pretty long day.
"Luckily I'm staying on site so you have the option of going back to the room. I didn't really do that too much yesterday though.
"As I showed yesterday and today, if you get off rhythm a little bit and you don't fully take advantage of the course, others will make up ground. Sunday will unfold and we will see what happens."
Oliver Wilson, who secured his first victory in 228 European Tour events at the Alfred Dunhill Links Championship last week, was among those to miss the cut in Portugal.