Otto stands at 10-under-par 134, four clear of Sven Struver and Fredrik Widmark, who are in the middle of their second rounds. Struver has played nine holes, while Widmark is through six.
Adilson Da Silva posted a 4-under 68 and is alone in fourth at 5-under- par 139. Alastair Forsyth is one shot back at minus-4 after his second straight 70.
The second round was delayed 2 1/2 hours due to high wind and eventually suspended for the night due to darkness. Play will resume Saturday morning at 8:00 a.m. local time.
Otto birdied the par-five third for the second straight day to get his round going. However, he gave that stroke back as he stumbled to a bogey on the fifth at Santo da Serra.
The South African atoned for that mistake as he birdied the par-three eighth. He nearly drove the 395-yard 10th, but came up 10 yards short.
Otto chipped in for eagle to jump to 8-under. After making bogey at the 12th on Thursday, he made birdie there in round two.
Two holes later, Otto made another birdie to get to 10-under before parring out.
'I am hitting the ball better now than I did five years ago, but my putting has let me down,' Otto admitted. 'It just goes to prove that if you make a few putts then you can succeed.
'My goal at the start of the week was to get into the top 10 to get into next week because I am not in the tournament next week at the moment, but if you play better than a top 10, then well done eh?'
Struver was even-par through nine holes with one birdie, one bogey and seven pars.
Widmark connected on back-to-back birdies from the second to get to minus-6. He parred the next three before played stopped for the night.
Raphael Eyraud shot a 1-under 71 to move into a share of sixth place at 3-under-par 141. He stands alongside Joakim Backstrom, John Bickerton, Michael Lorenzo-Vera, Mattias Eliasson and Miles Tunnicliff, who are in the middle of their rounds.
Three players are tied at minus-2, including Andrew Oldcorn, who shot 1- under 71 for the second day in a row.