The Italian has been suffering from muscle fatigue and was left out of recent games against Inter in the Coppa Italia and Napoli in Serie A in the hope that the rest would allow him to feature against Porto.
Head coach Andrea Pirlo confirmed in a press conference on Tuesday that Bonucci is not fit enough to play.
Juan Cuadrado had to be withdrawn early in the 1-0 loss versus Napoli due to injury and will miss this one as well as the weekend game against Crotone. That will allow two former Porto stars in Alex Sandro and Danilo to face their previous employers by starting in the full-back positions.
Giorgio Chiellini will likely partner Mathijs de Ligt in the centre of the backline.
There had been doubts over the fitness of Aaron Ramsey but he is set to travel, though likely won't feature in the starting XI.
Pirlo confirmed in his press conference that Paulo Dybala would travel with the squad to Portugal, too, but that he is not yet ready to play after suffering a knee sprain.
Arthur Melo will likely miss out due to injury.
Weston McKennie could be restored to a place on the right of the midfield, with Federico Chiesa on the left.
Adrien Rabiot and Rodrigo Bentancur should partner each other in the centre of the midfield four.
For Porto, they have issues in the full-back positions as Nanu has been missing after suffering a concussion against Belenenses, while Zaidu Sanusi only played 45 minutes of football at the weekend after previously injury his back. He could feature, however.
Otavio suffered a muscle strain in a cup game against Gil Vicente but also returned from the bench at the weekend, so could maybe feature off the bench.