Owen, who is still in search of a breakthrough victory on the European Tour, was two behind overnight leader Fredrik Jacobson to start the day. Owen played the back nine first at Vale do Lobo and birdied the 10th. He struggled with a bogey at the 11th, however, and lost further ground with a double-bogey at the 14th.
The 31-year-old regained some momentum with an eagle at the 17th to make the turn at 6-under. He bogeyed the second but ran off three consecutive birdies starting at the third to surge into the lead at minus-8.
Owen failed to save par from 10 feet out for a bogey at the sixth and looked to be in trouble at the ninth. Owen missed the green with his approach but managed to chip in for a closing birdie.
'I did feel a little unlucky then but then it all evened itself out with what happened at the last,' said Owen, who had missed a birdied opportunity at the previous hole. 'I was looking to finish three-four to be happy, but instead it was four-three, so it was the same result.'
Owen, who finished tied for third at this event last year, has yet to post a top-10 this season.
'I was nervous yesterday and there is going to be a few nerves tomorrow but I've been out in the last groups before and it is not as if I can't play in the last group,' said Owen. 'The most important thing is hitting fairways and if I can continue to do that, the numbers will add up themselves and we will see what happens.'
Jacobson also played the back side first and struggled with two bogeys over his first nine holes. The Swede two-putted for a birdie at the par-5 fifth but stumbled again with a bogey at the next.
The 28-year-old's problems continued at the par-4 eighth. Jacobson sent his tee shot out of bounds en route to a double-bogey and a round of 76.
'Today there was only really one bad shot in my round, the tee shot at the eighth which went out of bounds,' said Jacobson, who established a new course record with a 64 in Thursday's opening round. 'But the main difference from yesterday was my putter. It was so cold today, I just couldn't make anything.'
Jacobson finished at 4-under-par 140 along with Carlos Rodiles in a tie for third.
'I played awesome today,' said Rodiles, who shot a 71. 'I don't think I have played this good in a while. I had a lot of good birdie chances at the end but just didn't make any of them. But, on this course if you are putting for birdie everytime it is good, even if you don't make them.'
Brian Davis was one shot further back at 3-under-par 141.
Bradley Dredge, who won last month's Madeira Island Open for his first victory on the European Tour, posted a 73 to finish at 2-under-par 142 alongside Andrew Coltart, Jarmo Sandelin, Rolf Muntz and Charl Schwartzel.
Jamie Donaldson, David Lynn and Gordon Brand, Jr. tied for 11th at 1-under- par 143.
The 36-hole cut fell at 5-over-par 149 with 72 players qualifying for the weekend. Among those who failed to make the grade were Ian Poulter, Gary Evans, Robert-Jan Derksen and Lee Westwood.