The Blues argue that Valletta had six foreign players on the field of play when Hamza Barry replaced Edmond Agius on the 71st minute before Luke Montebello replaced Abdelkarim Nafti a few seconds later.
The game ended in a 2-2 draw. Alan da Silva put Valletta ahead on the 8th minute but a brace by Gianmarco Piccioni on the 15th and 65th turned the score in their favour before Lateef Elford-Alliyu equalised on the 78th.
The protest will be heard on Thursday at 17:30.