Otago was in the game up until the hour mark but Counties-Manukau scored three tries in the final quarter to run away a convincing 41-16 winner.
Brown said there were little things which in the end hurt his side.
"We had a couple of chances there but we made a couple of defensive errors and that let us down.
You can't afford to do that against a team like Counties who have some lethal attackers," he said.
"They scored some good tries but we also let them score a couple of tries."
Otago dominated the first 10 minutes of the second half and needed to get more than a return of three points from the boot of skipper Glenn Dickson.
"We had a bit of momentum there but we probably did not get enough points. We made a couple of small mistakes and then they came back down and scored.
They are a good momentum team and once they get on that they are hard to stop."
Otago could have skipped clear near the end of the first half when winger Buxton Popoali'i tried to run around the last defender when there was support inside him.
But Brown said he could not fault Popoali'i as that was what he wanted from his players - the courage to have a go and back themselves.
"Little things cost you in finals but you can't blame Bucky [Popoali'i] for that as that is the way we have played all year."
Despite the loss, Brown said it had been an awesome year with the promotion of club players into the first-class scene and getting people excited about the Otago team again.
"Many of these boys have come from nowhere at the start of the season and are now top-level rugby players. They may lack that bit of experience, and that probably cost us tonight, but they will be all the better for it.
"We will learn from it and come back next year all the better for it."
Brown said he had greatly enjoyed the year, and getting to coach young, keen players.
"It's been great helping these guys get better, and hopefully we have got a few players into Super 15 contracts.
"There has been a bit of a buzz around the team. What we did this year with the team in picking local players from club rugby I think really helped getting people back interested in Otago."
Brown will have a bit of time off before heading back to Japan next month to link with the Panasonic Wild Knights.
He will be back in Dunedin in March to start planning for he 2013 season.
