Otago had been thumped 41-0 by Hawkes Bay in a Ranfurly Shield challenge last week but it made that a distant memory with a solid 80 minute effort.
It led 20-7 at the break and never gave the visitors a sniff in the second half, scoring the four try bonus point with 10 minutes to spare.
Hayden Parker helped himself to 23 points and was the catalyst for much of what Otago did right.
The win puts Otago back in the running for the top four of the championship in the ITM Cup.
Waikato kept up its up and down season and never fired a shot in the entire match.
Otago 38 (Tom Franklin, Tei Walden, Hayden Parker, Fa'asiu Fuatai tries; Parker 3 con, 4 pen) Waikato 7 (Damian McKenzie try, con) Halftime; 20-7.