Cooper hit a sublime unbeaten 108, hitting 12 boundaries in the 131-ball knock, leading Waikato Valley to 243.
In reply, Northland had a few contributors with Bradley Kneebone (27), Ian Page (29) and Todd Beehre (20) all getting starts.
Rory Christopherson was the pick of the batsman with 37, but no one kicked on as Waikato Valley's attack slowed them down.
Keith Vincent (3 for 32) and Joshua Malpas (2 for 20) were the pick of the bowlers as Northland were bowled out for 186.
This gave Waikato Valley first-innings points and a 57-run lead. This was the first time in Waikato Valley's history they had managed a first-innings victory over Northland.
Waikato Valley batted through to 94 for three in their second innings, but with no outright result in sight the captains shook hands and walked away.
Northland's next match is against Counties on February 18-19.