Rafael Benitez felt Newcastle should have received more protection from the match officials after Cardiff pushed the Championship leaders all the way at St James' Park.
The Magpies had gone into a two-goal first half leader when Christian Atsu's third-minute opener was followed by Yoan Gouffran's strike moments before half-time.
After the restart - and a few missed chances from Newcastle - Cardiff rallied and pulled a goal back with 13 minutes to go through Peter Whittingham.
That goal arrived after Marouane Chamakh had appeared to handle the ball in the build-up, which incensed the Newcastle players, and Cardiff were unlucky in the end not to leave with a point.
But Benitez, relieved with a victory that leaves his team eight points above the play-off zone, thinks referee Tony Harrington should have blown his whistle more often against a Cardiff team up for a battle.
Benitez said: "It was a Championship game. We started well, had chances and scored two, and started the second half well ... but we didn't do it.
"Then they started with the long balls, throw-ins and free kicks. The ref allows too much contact. They were complaining and we were not happy with decisions.
"We have to work hard even if we concede a goal that is not correct. I was not happy that we had to defend so much. But if a ref allows this situation you have to defend.
"I would rather play passing football, getting goals. In football if you play well you will have chances to win games. Sometimes you can't because the opposition is aggressive and the ref allows this contact.
"If you can it means you are strong as well. Sometimes you play passing football, sometimes you have to be strong and defend and stand up."
Benitez was not the only manager to have his grievances, though. His counterpart Neil Warnock, who had a row with Benitez nine years ago when Sheffield United went down, felt Cardiff should have had a late penalty.
Warnock, who only took over at the beginning of last month, was furious Cardiff were denied a spot-kick to equalise. He claimed Aleksandar Mitrovic "mauled" down Sean Morrison.
He said: "He gets kicked in the face. I am so gutted at the penalty. Mitrovic mauls him down. At this level the officials should be educated better and know about the pull.
"To add salt the linesman gives the free-kick to them. They will go home and see it with their coaches next week and say 'oh yeah, I made a mistake'.
"We have not got enough goals in the squad at the moment. We have to work on that. There were some pluses though. The lads at the back especially. At half time they might have got five or six. The second goal killed us."