The France international was omitted from the Magpies squad which travelled to Anfield on May 11, with an ankle injury given as the official reason for his absence.
But the striker told L'Equipe on Tuesday that Pardew had agreed to leave him out of the Liverpool match as a precaution ahead of this summer's World Cup with France.
"The coach Alan Pardew understood my point of view," Remy said. "We had nothing to play for and I didn’t want to risk getting hurt again."
In a statement published on Newcastle's official website, Pardew insisted: "Any suggestion that I colluded and agreed with our loan striker, Loic Remy, that he did not have to play in this game are wholly untrue.
"To suggest that I considered there to be nothing riding on that game is also completely false. Our final league position was at stake, as was the race for the Premier League title for our opponents, Liverpool.
"What is more, each and every one of us associated with the club was desperate to get a result for our supporters, especially those 2,800 travelling fans who made the journey to Anfield that day.
"The reality was that Loic had sustained an ankle injury in our game against Cardiff the previous week. The results of an MRI scan conducted after that fixture revealed ligament damage and swelling around the joint.
"It was a result of this injury, and the fact that Loic was unable therefore to complete any training session during the week leading up to the Liverpool game, that meant he was not fit for selection.
"Had Loic been fit then clearly, without question, he would have been selected to play in what was a crucial game like every other."
Pardew's position as manager has come under intense pressure in recent months as a result of a disastrous second half of the season, which saw Newcastle win just five of 20 matches in 2014.