Kinnear made a surprising return to the club earlier in the summer after being asked back by owner Mike Ashley and he angered fans with claims about his previous achievements while also mispronouncing player names.
It has been suggested the former Newcastle boss could undermine Pardew, who came under pressure last season after narrowly avoiding relegation having only signed an eight-year contract in September 2012.
But Pardew insists he will be responsible for managing the team and Kinnear's duties will be focused on transfers, such as the ongoing pursuits of Lyon striker Bafetimbi Gomis and Queens Park Rangers' Loic Remy.
"I think initially people thought Joe was definitely babysitting for me here, for things not to go well and Joe to become manager," said Pardew in 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."
Meanwhile, Pardew is hoping Ashley will soon progress with a blueprint to improve Newcastle's training facilities as they seek to follow the lead of Europe's elite clubs.
"We've got plans, which I hope Mike will give the go-ahead for, because we've fallen behind some of the top sides in term of facilities, especially water-based recovery," he said.