Jun had a 12-under 276 total on the Cleveland Heights course.
Lindberg finished with a 72, and 16-year-old Florida amateur Victoria Kiser (69) was third at 10-under. Canadian amateur Kira Meixner (70) and Molly Birmingham (72) followed at 5 under.
The 94 players who made the 54-hole cut will receive exempt or non-exempt status for the 2009 Futures Tour. The number of exempt players will be determined following the final stage of LPGA Qualifying School in early December.
Jun, the Canadian PGA Womens Championship winner in August, had two birdies and two bogeys in the final round.
I made a lot of pars today, but I just didnt hit the ball close enough for birdies, Jun said. I didnt really know how I was standing during the day, so it was easy to not think about it and just play my game.
Jun is headed to the final stage of LPGA Tour Q-school in December. She tied for 25th last year to earn non-exempt status.
I learned I was a lot more patient as a player than I thought because I didnt get off to a great start, Jun said. I felt like things could have gone really bad, but they didnt.
Lindberg, a senior at Oklahoma State, missed a 5-foot birdie putt on her last hole.
I missed a lot of putts, but I was hitting it close all day, Lindberg said. I knew I could have had a lower score today, but I had a great experience all week. Its going to be a while before I play another tournament, but I feel really good about the way I played.