The Englishman, who started the week as the fourth reserve, finished 36 holes on Friday at 8-under-par 136. Little is one ahead of first-round leader Nick Dougherty (71), Mark Foster (69) and Charl Schwartzel (68) at Centro Nacional de Golf.
This tournament is very far behind schedule after heavy rain on Thursday forced a suspension of nearly eight hours. Friday also saw a stoppage, a two- hour delay for lightning, and half of the field has yet to tee off in round two.
They will play as much golf as possible on Saturday, although inclement weather is once again in the forecast.
Englishmen Simon Dyson (69) and Andrew Raitt (70) are in the clubhouse at 6- under-par 138.
Marcus Fraser and Richard Bland are tied for seventh place at 5-under par, but have not completed their second rounds. Gregory Bourdy is at minus-5 and has not yet teed off in the second round.
Little did not hit a ball in competition on Thursday and played his opening 18 in 5-under 67. The left-hander began his second round after a 30-minute break and teed off on No. 10.
He birdied his first two holes of round two, then parred his next three. Little bogeyed the 15th, a hole he birdied in round one, but answered with a birdie at 16, a hole he bogeyed in the opening round.
Little bogeyed 17, but got back to 7-under par for the championship with a birdie at the first. He rattled off back-to-back birdies at four and five, both from close to 9 feet, to become the first player to reach 9-under par.
Little did not last long at 9-under par. He bogeyed the seventh, another hole he birdied in the first round, but stands on top after a very long Friday at the course.
'It's been a very, very long day,' said Little. 'To come away after 36 holes at 8-under par has been enjoyable. We only had to stop once during the second round so in terms of our breaks from golf, it hasn't been too bad compared to the other side of the draw.'
Little lost his playing privileges last year after a 2005 season that saw him finish 65th on the Order of Merit. Last year, he finished 150th and could not get his card, so he knows he has to take advantage of his chances.
'I've got to seize the opportunity,' said Little, who will play a combination of the European Tour and Challenge Tour. 'It won't be easy as we all know. I'm looking really forward to putting a good performance into the weekend.'
Foster combined four birdies and a bogey in round two, while Schwartzel mixed an eagle, three birdies and one bogey.
Dougherty had an interesting first round as both playing partners, Peter Hedblom and Jose Manuel Lara, withdrew. He finished the round as a single, then Dyson joined him in round two.
'It was a unique experience, especially behind three-balls,' said Dougherty. 'It made me slow my timing and tempo down. All in all, I don't think it was a disadvantage.'
Defending champion Niclas Fasth (72), Graeme McDowell (69) and Terry Price (70) are in the clubhouse at 4-under-par 140. Fredrik Andersson is on the course at the number, while Notah Begay III, Luis Claverie and Graeme Storm are at minus-4, but have not teed off yet.