Rufer was sent off in the second half of the Phoenix's 1-1 draw for a challenge on Denis Genreau, where he originally won the ball but then caught the Bulls midfielder's legs as he attempted to run clear.
Referee Stephen Lucas had originally booked Rufer but after consultation with the VAR official, decided to show a straight red card for violent conduct.
Wellington were fuming over the call, with Phoenix general manager David Dome saying A-League officials had admitted the decision to send Rufer off was incorrect.
The MRP reclassified Rufer's offence on Tuesday from "violent conduct" to "serious unsporting conduct," with Wellington accepting the resulting one-match ban that rules the midfielder out of their next match against Newcastle.
"While disappointed that the red card was issued in the first place, I think this result is the best that we could have expected," Dome said.
"The downgrading of the offence by the Match Review Panel is a common-sense approach and the MRP must be congratulated on this action.
"We will now move on and prepare for our home match on January 24 against Newcastle Jets."