A printer includes a printhead cleaning system that enables improved cleaning of the printhead and reduces nozzle contamination. The printer includes a pair of parallel walls and an elongated member extending through at least one of the walls. The elongated member is connected to a vacuum source and has a slit positioned between the pair of walls. A controller is operatively connected to the vacuum source and to an actuator, and operates the actuator to move a printhead into contact with the pair of walls to place a face plate of the printhead opposite the slit. The controller further operates the vacuum source to generate a vacuum in the elongated member to pull air into the elongated member when the printhead is opposite the slit.