Echenique reached 10-under 132 to sit ahead of a trio that included overnight leader Martin Kaymer of Germany, who shot a 72 after tying the course record with a 62 on Thursday.
Charl Schwartzel of South Africa (66) and Steve Webster of England (65) were also two strokes back.
When I saw myself atop the leaderboard, I enjoyed the moment, said Echenique, who finished second at the BMW International Open in Munich last week after making a double eagle on the 72nd hole. I have a good moment now. I have to enjoy the moment. My tee shots were very good today.
Several big names missed the cut of 143, including Masters winner Angel Cabrera (145), Jeev Milkha Singh of India (145), three-time major winner Padraig Harrington of Ireland (147) and 2005 U.S. Open winner Michael Campbell of New Zealand (154).
Echenique bogeyed his opening hole but recovered with an eagle and four birdies on his front nine.
Kaymer, meanwhile, only made one birdie to go with two bogeys ' including on the 14th when he landed in the rough twice on the longest hole on the course.
I was not really happy with my game today, the German said. I didnt really have the right numbers to go for the flags. So I had to play a little more defensive. I didnt really put myself in a good position to make birdies.
Peter Hanson of Sweden was tied for fifth place with Richard Green of Australia on 135.
Harrington missed his fifth straight cut and is struggling to rediscover his confidence before defending his British Open title in two weeks.
I need to work on the putting for the next two weeks, Harrington said. I need to putt better than I did this week. Thats where the focus will be. A few wedge shots as well.
Lee Westwood was four shots back in seventh place, while European Ryder Cup captain Colin Montgomerie shot a 74 to sit 11 strokes behind.
John Daly, who pulled out during the opening round Thursday because of back pains, said he would only need a few days to recover.