The Addicks could easily have taken the lead in the first half through Scott Wagstaff and later Johnnie Jackson, but at the other end goalkeeper Rob Elliot did well to deny Andy Bond and ex-Charlton loanee David Mooney.
The two sides, who contested a 3-3 stunner on New Year's Day, somehow eclipsed the drama of the previous month in the second half thanks mostly to a stunning series of decisions from the official.
Steven Gillespie had the ball in the Reds' net only for the referee to blow his whistle for a foul by David Mooney, give the goal after consulting his assistant and then strike it off once more, giving instead a drop ball on the edge of the area.
And moments later, Wright-Phillips won the game with a beautiful overhead kick from Wagstaff's cross to send the travelling fans into further frustration.
Seven additional minutes were played and Mooney had an effort cleared off the line by Alan McCormack in the final minute as Chris Powell's men held on and made it two wins from two for the new boss.