Lowe led the Deepdale club to respectable 13th, 12th and 10th placed finishes in the second tier during his three seasons in charge.
But Preston lost their Championship opener 2-0 at home to Sheffield United on Friday and, after discussions with the board on Sunday, the 45-year-old has made a surprise exit.
Mike Marsh, Peter Murphy and Ched Evans are set to temporarily take charge of the team for this week's matches with Sunderland and Swansea.