The Warriors winger scored at the start of each half in an influential display at the DW Stadium that also saw him set up Darrell Goulding and kick two goals.
But his second try, with the score at 10-10, was contentious and sparked much debate as to whether he had grounded the ball in the corner.
Wigan went on to secure the win through Anthony Gelling but Rovers, after earlier scores through Greg Eden and Michael Dobson, set up a tight finish through Evarn Tuimavave.
It was a much more competitive performance from Rovers after conceding 130 points to the Warriors in their two previous meetings this season.
Sam Tomkins was ruled out with a virus and without him Wigan laboured for most of the first half, although they started and ended it well to lock the scores at 10-10 at the break.
Charnley – once of Hull KR – showed his pace with a burst down the right to release Matty Smith in the opening minutes, but the Wigan scrum-half was stopped short.
Rovers were forced into a change when Jordan Cox was hurt in a heavy tackle and, after lengthy treatment, helped from the field wearing an oxygen mask.
Wigan claimed the lead as quick hands from Tomkins’s replacement Ryan Hampshire created an overlap for Charnley to dot down in the corner.
The Robins were determined to stand up to Wigan this time and responded positively, forcing a dropout and applying more pressure before Dobson sent Eden over.
Dobson added the conversion to give his side the lead.
Hampshire broke from deep to set Charnley clear but Eden halted the winger short.
Rovers extended their advantage when Dobson took a high pass in his stride and weaved his way through the Wigan defence to score.
The visitors then showed their resilience to keep Wigan out, stopping Epalahame Lauaki on the line and preventing Dom Crosby touching down.
But they could not hold out until the break. Smith’s clever kick wide bounced perfectly for Charnley and his pass inside gave Goulding a run to the line. Charnley’s goal levelled at the interval.
Controversy erupted early in the second half as Charnley finished a fine move in the corner with a one-handed stretch for the line.
The winger was convinced he had held off Eden’s attention just long enough to squeeze the ball down in the corner and, after lengthy deliberation, video referee James Child agreed.
Rovers may have had a case for believing the ball had brushed the whitewash, and so they may have feared the worst when Charnley claimed another in front of the deadball line moments later.
But this time Child ruled David Hodgson’s had been the first hand to make contact.
Wigan began to resemble something more like themselves as debutant Joe Burgess threatened to score on the left.
Rovers were again frustrated by the video referee when Child could find no reason to award Hodgson a try in the corner.
Wigan made sure of victory when Gelling crashed through a weary Rovers defence, Charnley converted and Smith added the extra insurance of a drop goal.
Tuimavave crashed over to set up a tense final few minutes but Wigan were not to be denied.
Wigan: Hampshire, Charnley, Goulding, Gelling, Burgess, Green, Smith, Mossop, McIlorum, Taylor, Hansen, Tuson, O’Loughlin. Substitutes: Hughes, Lauaki, L. Tomkins, Crosby.
Hull KR: Eden, Hall, Gleeson, Salter, D. Hodgson, Burns, Dobson, Paea, J. Hodgson, Walker, Lovegrove, Cox, Mika. Substitutes: Withers, Beaumont, Hepi, Tuimavave.
Referee: R Silverwood (RFL).