The pair pulled far away from the field with their performances in Texas, setting up a two-way contest in Sunday's final round.
Dufner, seeking his second straight tile and his third in five weeks, finished three rounds at 15-under 195. He has held the lead in 12 of the last 35 rounds he's played.
Johnson was right behind at 14-under after firing a 5-under 65. He had a chance to tie the contest on the 18th hole but just missed a putt for birdie putt.
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