Guardiola and his staff were on their feet demanding a penalty for a first-half challenge on Phil Foden, and Newcastle's winning goal was the subject of a long review for a number of possible infractions in the build-up before it was allowed to stand.
"It is what it is after VAR decided. They know perfectly," Guardiola told the BBC, adding that he had "no questions" despite talking to the referee after the final whistle.
The opening 45 minutes saw both sides miss plenty of opportunities, and all the goals came between the 63rd and 70th minutes as Newcastle's Harvey Barnes struck twice, either side of a Ruben Dias equaliser for City.
"Both keepers were good and after we missed chances," Guardiola said. "It was an entertaining game with many chances, we were closer in the beginning."
The defeat denied City the opportunity to close the gap on Arsenal, who top the table on 26 points, with City now third on 22 points, having played one game more.
"Newcastle is a top side, top players, top manager, so unfortunately tonight we could not make the momentum that we had," Guardiola said.
"It was an entertaining game, we both had chances, and then there was a momentum shift, and ultimately we couldn't win."
For 14th-placed Newcastle's goal-scorer Barnes, a rare win over City was just what the club needed after a slow start to the season.
"Hopefully after today's result we can kick on and go on a good run," he told the BBC.