The landmark ton was brought up off a McClenaghan short ball, pulling it to the ropes to the delight of his teammates.
Cooper was particularly pumped up about reaching 100 and rightly so, fist pumping before raising his helmet.
Cooper said while it was pretty great to bring up the milestone, he felt that he left more out in the middle and it wasn't all easy going.
"I'm feeling all good now. Walking off I was pretty tired, it was a long stint out there," he said.
"I was pretty gutted I didn't turn it into a big one and get us into a great position but once you sit and reflect on it, it was pretty awesome to bring up my first ton.
"Battled some real demons out there. I was struggling a little to find my timing for my whole innings to be fair.
Broke two bats while batting, that's how bad my timing was at times. But you have to ride the waves. In the past I would have got myself out but now it's grinding it out.
"Nothing comes easy at first class level."
Unfortunately Cooper was out the next delivery, caught behind off McClenaghan after his 374-minute vigil.
He said the attack which included Black Caps Lachie Ferguson and McClenaghan made it tough, but having a quality batsman with him helped no end.
"Lachie and Mitch were getting it to reverse. It was tough to play near the end especially for guys who weren't set," he said.
"Played a little against Lachie through A's and he's taken his game to the next level. He's quite the handful with variable bounce. Mitch was also very handy and had it reversing. They did not make it easy.
"Having Corey out there helped heaps. When I was struggling he was great to have out there. He's world class in his own right and takes off any scoring pressure you have.
"He's pretty awesome to bat with and on top of that he's a champion bloke."
Over the first four sessions Auckland made an intimidating 465 following half centuries from Robbie O'Donnell (75), Nethula (52), McClenaghan and Rajvinder Sandhu.
McClenaghan (73 not out) and Sandhu (82) made the Northern Districts attack work for their wickets, putting on 139 for the final wicket. The pairing smashed 15 boundaries and six sixes in their 28 over stand.
Scott Kuggeleijn (4 for 89), Daryl Mitchell (51) and Ish Sodhi (3 for 146) shared the wickets.
Cooper managed to take two catches in the innings.
In reply, Northern Districts scored 334 largely on the back of Cooper and Anderson.
Sandhu (4 for 29) and Nethula (4 for 70) provided carnage with the ball to leave Northern Districts 131 runs short of first innings points.
Auckland then set about building a substantial lead to take into the final day's play.
James Baker (2 for 27) removed both openers relatively cheaply but new Black Cap Glenn Phillips went on the counter-attack.
Auckland ended day three on 151 for 2, with Phillips on 86 and Rob Nicol on 24. They lead by 278 runs going into the final day.
Cooper said the mindset for Northern Districts is pretty clear, especially after Canterbury's innings victory over Otago.
"We want to win. That's our mindset. We're going to have to chase a fair bit but we've got the batting order to do it," he said.
"We really need the win to keep us afloat in the competition. It isn't completely over if we don't get up but a win will definitely help."
