Wilkinson had four birdies, three bogeys and a double bogey during his third round of 73, which he played at the Spyglass Hill Golf Course, as he fell down the leaderboard. He was projected to drop to 159th in the FedEx Cup standings.
Lee, the best-performed New Zealander on tour this season, made two eagles, four birdies and four bogeys during his four-under 68 at Pebble Beach today but it wasn't enough to help him make the cut.
The 24-year-old was projected to drop from 38th to 44th in the FedEx Cup standings. The top 125 in the standings at season's end retain their cards for next year.
The Pebble Beach event, which features some notable celebrities in the pro-am, including actors Bill Murray and Andy Garcia, is played across three courses and features a 54-hole cut where the top-60 players plus ties contest the final day.
American Jim Furyk holds the lead after thee rounds at 18-under.