He said St Peter's were clinical in punishing his side's mistakes.
"They're a very big, structured side with good key players across the field. They capitalised on our mistakes, as a good side always will.
"We showed a lot of heart. We had six injuries from last weekend, so we had to call up some second XV players and we had backs playing in the forward pack.
"I thought to show the heart they showed was pretty good under those circumstances, it goes to show what a good team we've had this season."
Pedersen said he was "very happy" with the season.
"If someone had told me that we'd be Bay champs and in the running for top-four NZ co-ed at the start of the season I would've said they were lying. It's a bit unbelievable to be honest.
"It's the brotherhood they've got, the team are very close on and off the field and they do have a lot of belief in themselves and the structures the coaches have put in place.
"That's been pretty gratifying really, to watch how far they've come as men," he said.
Rotorua Boys' coach Ruki Tipuna said his side started and finished well against Hamilton, but lapses in the middle of the game cost them.
"We got beaten up in the third quarter and that's where we lost it. They were very clinical, they don't make a lot of errors," Tipuna said.
He said this season, finishing third in a tough Super 8 competition and beating Tauranga Boys' College in the Baywide final, was a good experience for his players, but was realistic about the need to be better next year.
"Given the amount of young boys we have it was pretty good on the whole, but we would've wanted to make top four.
"We don't want to be saying that again next year or the year after. We've had our year of calling ourselves young, so we have to get into it next year and make sure we go one better," he said.
