Ko dropped another shot at the par three 11th before making consecutive birdies again on 13 and 14 and then parred her way home to sign for a 69.
Meanwhile, Hamilton golfer Steven Alker faces a nervous weekend as he waits to see if he has done enough to earn a PGA Tour card for 2014.
The 42-year-old, who opened with an even par 71 at the Cox Classic of Omaha on the Web.com Tour to be in a share of 103rd place, carded a four-over par 75 in round two to miss the cut at a crucial time.
The result means that Alker's chances of qualifying are now out of his hands. On the current standings he is projected to slip from 22nd to 24th on the Web.com Tour money-list.
The top-25 players at the end of the Cox Classic on Monday morning (NZT) automatically qualify for the PGA Tour in 2014.
But Alker's position could so easily change in the final two rounds of the final week of the regular season on the Web.com Tour.
The Kiwi, who won the Utah Championship in July to turn his season around, had a round to forget at the Champions Run Golf Club when it mattered most.
He showed early signs of nerves when he double bogeyed the second hole. He rallied with two birdies on four and five before carding three straight bogeys to make the turn in three-over par 38.
By then he was well off the cut mark and he closed with two bogeys and a birdie to worsen his position.
Following this week, the top 25 will be joined by another 25 players who earn their way onto the game's most lucrative tour through a new four-tournament playoff concluding with the Web.com Tour Championship from September 26-29 on Dye's Valley Course in Ponte Vedra Beach, Florida. The four-week playoff takes the place of the tour's annual qualifying tournament.
Alker is hoping to join Danny Lee and Tim Wilkinson who have already qualified for the PGA Tour.
Lee, playing in his final Web.com Tour event, also missed the cut in Nebraska with rounds of 72 and 71.
On the European Tour, Michael Campbell missed the cut at the Johnnie Walker Championship at Gleneagles in Scotland. Campbell was six-over after 36 holes, nine shots back from the cut line.
In Japan, Michael Hendry shot a three-under 69 in his third round to be in a share of 21st at the Kansai Open with around 20 players still to finish their round today. Fellow Kiwi David Smail missed the cut after rounds of 75 and 73.