Northland, despite the driving downpour, had their opportunities early but handling errors and lineout woes proved costly.
The Taniwha were enjoying the lion's share of possession but Counties were more than up to the task defensively as their opponents lacked real impetus in their carries.
Counties made sure their rare forays into Northland territory counted as Tim Nanai-Williams rushed over from fullback to extend their lead.
Northland missed a late first half chance as flanker Jack Ram couldn't control the ball but Breen continued his perfect season with the boot to make it 12-6 at the break.
A dropped ball from the kickoff put Northland under immediate pressure but in what has become a staple of the side, they defended stoutly and forced the turnover.
They were rewarded a few minutes later as a raid into Counties' red zone led to a brilliant running line from Blake Hohaia put him under the posts for a converted try.
Straight off the kickoff, Northland failed to make a good exit play which cost them three points through Baden Kerr's boot.
Another Breen penalty goal gave them back the lead but again the lead didn't last.
A brilliant turnover from openside flanker Fotu Lokotui inside Northland's 22 put Counties on the offensive and former All Black Stephen Donald was right there to race over the tryline.
Luteru Laulala added a penalty with five minutes to go, giving Northland a nine point buffer to try and overcome.
Northland tried in vain to pick up a vital competition point but Counties defence continued to be too clinical.
Counties-Manukau 22 (Albert Nikoro, Tim Nanai-Williams, Stephen Donlad tries, Baden Kerr con, pen, Luteru Laulala con)
Northland 16 (Blake Hohaia try, Peter Breen con, 3 pen)
HT: 12-6