Assistant manager Carver, who was in charge of Newcastle on Saturday due to Alan Pardew's stadium ban for headbutting Hull City's David Meyler, was left disappointed as the Premier League's bottom side secured their seventh league win of the season.
Ashkan Dejagah scored the only goal of the game after 68 minutes, but Carver felt referee Howard Webb had missed a foul on Luuk De Jong in the build-up to the game's key moment.
Newcastle's frustration increased in stoppage time when John Heitinga appeared to handle inside the penalty area, but Webb opted to blow for full-time rather than award a penalty.
Carver said: "It's been a difficult day, I can't fault the lads for their effort, but we lacked quality.
"The game hinged on a few key decisions.
"(In the build-up to Fulham's goal) Luuk De Jong gets caught from behind, we defend poorly, he (Dejagah) cuts inside and we lose the game.
"I am disappointed with the decision on Luuk but that's how it is.
"I certainly counted to 10 (to control his anger), but we have to, we have to be on our best behaviour.
"I had a conversation with Howard (Webb), he explained his reasons to me and I accepted that."
Carver confirmed that Pardew had watched the game in a hotel room and that he kept in contact with the Newcastle boss during the match.
"I spoke to him coming off the pitch at half-time, and spoke to him towards the end of the game, probably two conversations and that's it," he said.
"I don't know how heated he was, he was really calm at half-time.
"We spoke at full-time, he informed me to look at penalty decision, and have a look at the challenge, which I did, it was pretty brief."
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