Kinnear was controversially appointed to the role in June by chairman Mike Ashley, with his arrival leading to suggestions that Pardew could be facing the sack.
But, while the English boss has admitted to previously harbouring concerns over Kinnear's remit, he insists the pair can work well together.
"I think initially people thought Joe was definitely babysitting for me here, for things not to go well and Joe to become manager," he told The Times.
"I think that's what people's first perception was. And I have to say it was a perception I was a bit concerned about, too.
"I needed to speak to Mike and Joe about that and say, 'I was given an eight-year contract here and I don't want any interference'.
"I will always manage one way and that is talking to my staff, talking to my players, talking to my peers, as well as people like the owner, to make sure we are on the right agenda.
"Joe now fits in there. But he can't interfere with me managing the team and I won't let him. I made it very clear to Joe."
Kinnear previously managed Newcastle on an interim basis during the 2008-09 season before stepping down to undergo heart surgery.