The Eagles had been pushed for a late equaliser before Liverpool were given a late spot-kick.
Odsonne Edouard’s 55th-minute tap-in had given the Eagles hope of taking points off Jurgen Klopp’s side, who started brilliantly in south London and scored twice in the first half through Virgil Van Dijk and Alex Oxlade-Chamberlain.
A grandstand finish had been set up at Selhurst Park after Palace pulled one back but an innocuous coming together between Diogo Jota and Palace goalkeeper Vicente Guaita saw the Reds awarded a spot-kick, which Fabinho dispatched to put the game to bed a minute from time.
“I think we give ourselves the best chance to get something from the game but obviously that decision by the referee took our hope away, that poor decision from the referee took our hope away,” Vieira said.
“The reason is having those meetings with the referee and explaining to coaches that contact is part of the game, so that if there is a situation like that and there is not an obvious contact, there will not be a penalty.
“This one here and when you look at the situation with Jota, who I believe was really quite smart, but at the same the referee was naive or the VAR I should say was naive.
“There is no way that Jota could get the ball back and score or that Vince tried to stop. There is no way Vince and Jota cannot have contact because of the situation they were in.”
Opposition number Klopp was less forthcoming about the incident which occurred in the 85th minute with Jota played through on goal only to miss his kick and collide with Guaita in the aftermath of his failed attempt.
The Liverpool boss said: “I didn’t see it but Jota thought it was a penalty, I could see that on the pitch.
“VAR thought it was a penalty and that is why the referee went to the screen so I am not sure what we are talking about now? Four eyes watched it.”
Klopp was at a loss to explain why Liverpool lost their rhythm after dominating the opening 35 minutos.
It had been a taxing week for the Carabao Cup finalists, who booked their place at Wembley with a 2-0 win over Arsenal on Thursday and had seen off Brentford by a 3-0 score last weekend.
A fourth win without Mohamed Salah and Sadio Mane this month helped the Anfield club close the gap at the top of the Premier League to nine points after Manchester City, who have played a game more, were held to a 1-1 draw by Southampton on Saturday.
“The first 35 minutes was brilliant and some of the best stuff we have played all season. Exactly the way we want to play and if somebody had an explanation for what happened after 35 minutos, I would like it,” Klopp added.
“I don’t understand but 100 per cent a bit of a fatigue problem but we are not the first team to have that. Obviously after being 2-0 up and after a super intense week, we just decided to have a little break on the pitch but that is not possible.
“In these moments the chances Palace had were all set up by us pretty much, we gave the ball away in the wrong moment and these sorts of things, so that is what happened but why?
“If we had played the 90 minutes how we started it would have been a tough afternoon for Crystal Palace and it could have been a draw or whatever, so I am over the moon with this result, it was so important for us.”