Brisbane escaped with a narrow four-point win, but Fagan said victory was soured following Nick Robertson's comment against the Suns earlier in the week.
"I'm disappointed with Nick Robertson's comments about the Gold Coast Suns, it's not what we think about them and it's not what Nick thinks about them either, he just got carried away.
"It sort of takes a little bit of gloss off it.
"I know it adds a bit of spice to the game from an observer's point of view, but that's not the way we want to conduct our business."
Fagan went on to apologise to Gold Coast and said Robertson would learn from his mistake.
"I love the spice and the hard contest but it's not going to become a clash where the Brisbane Lions trash
"If we lost we would have copped our right whack.
"He's learnt a lesson and hopefully everybody at our club has. It's not something that has happened before."
Fagan described the win as a "grind", saying it was a relief to finally squeak out a close game.
Brisbane had to fight back from nine points down early in the final term with the tide against it, before goals from Allen Christensen, Dayne Beams and Lewy Taylor swung the match.
After five losses by seven points or less, it was the first time this year Fagan's men had won a close contest.
"It was good in a sense to grind away and win a game," he said.
"It didn't look good and our boys found something. With all the close losses this year … it's good for them to get over the line in one of those games."
Fagan said he was pleased with Dayne Zorko's effort, finishing with 17 touches and nine tackles amid the constant attention of Touk Miller.
Fullback Harris Andrews spent time in the
Fagan said he'd been hoping to see how Andrews performed up forward for quite a while.
"I've been dying for two years to put Harris up in the forward line to see how he'd go," Fagan said.
"Everyone tells me he's a pretty handy forward, so I thought why not give it a go when we were struggling.
"It was good tonight to throw Harris up there."