Santos had a one-shot lead after the first round and got off to a strong start on Thursday. He had three birdies on his first four holes but bogeyed the fifth before mixing in a bogey and two birdies on the back nine as the wind picked up.
"Struck the ball very well today. I just missed a few shots but still happy with the round," said Santos, the 2012 European Tour rookie of the year. "This afternoon, the wind is a little bit stronger than the morning, so I'm happy with 2 under this afternoon. Yesterday, you could reach the 16th; today, no. So I think it's a big difference with the wind."
Justin Rose, who finished second last week in Abu Dhabi, was in contention early on with two birdies on his front nine but two bogeys coming in dropped him to 5 under overall and a tie for 20th.
Several big names missed the cut at 1 under, including last year's winner and former British Open champion Paul Lawrie and Europe's new Ryder Cup captain, Paul McGinley.