It is the fifth time Dufner has led a tournament on the PGA Tour this year, most recently doing so at the 36-hole mark of the Zurich Classic in New Orleans. He went on to win that event for the first victory of his career.
Dufner shot a 4-under 66 Friday with birdies on four of the last five holes to equal the low round of the day. He finished 36 holes at the TPC-Four Seasons course in 7-under 133.
Kuchar bounced back from a slow start to fire a 68 in his bid to become the first back-to-back winner on the tour since Tiger Woods captured two tournaments in a row in 2009.
Defending champion Keegan Bradley was part of the group at 135. Phil Mickelson hit his tee shot in the water at the 18th and suffered a double bogey that left him at 139.
In addition to New Orleans, Dufner led the Phoenix Open and the Transitions Championship. He then shared the 36-hole lead with Fred Couples at the Masters before fading on the weekend.
Dufner also came close to winning the PGA Championship last year before losing to Bradley in a playoff, and his record since then has vaulted him from relative obscurity to the No. 21 spot in the world rankings.
It took a score of 2-over 142 to make the cut. Among those missing the weekend action will be former champion Adam Scott along with Masters runner-up Louis Oosthuizen.