The win lifts Canterbury into fourth place on the NZFC table with Otago now trailing a point behind in fifth place.
Otago faced a torrid start to the match as Canterbury handled the gusty wet conditions better and mounted attacks that penned the home side in its own half.
Otago coach Malcolm Fleming chose to play a three-man defence of Mike Abbott, Tim Horner and Tristan Prattley because of the recent return to England of centreback Chris Jenkinson and injuries to Tom Sadd and Dave Shaw.
More injuries ruled out striker Dave Dugdale and midfielder Robbie Deeley, and it was a case of too many absentees and too many changes.
"Our problem was lack of cover from midfield.
Not enough guys picking up Canterbury runners, and consequently we struggled in the first half," Fleming said.
Certainly Otago was at sixes and sevens when Aaron Clapham headed the ball back across the goalmouth for striker Russell Kamo to score at the far post after 19 minutes.
Canterbury played its typical passing game with success in the difficult wet, windy conditions.
A typical error gave Canterbury possession after 31 minutes and, against turning defenders, a two versus one situation set up striker Tom Lancaster to sidefoot Canterbury into a 2-0 lead.
In response, Otago rebounded with some incisive play with Nathan Knox carving along the left touchline and cutting the ball back for Dan Ede to shoot Otago back into contention at 2-1 after 33 minutes.
As half-time approached, Canterbury forged further ahead when Kamo finished off another pacey attack to make the score 3-1 and intensify coach Fleming's half-time team talk.
Otago played better in the second spell.
Knox should have narrowed the score, but missed an open goal, then later almost atoned with a powerful volley that hit Canterbury's crossbar.
In the closing stages, Otago also earned a series of free kicks and corners, but the Canterbury defence, well led by Gareth Rowe and Dan Terris, held firm.
"The better team won on the day," Fleming said.
"We played better in the second half, but we have got some hard work ahead before we play Manawatu away on the 9th."
Meanwhile, Waitakere United increased its lead at the top of the table despite Hawkes Bay United snatching a dramatic 2-2 draw in Napier yesterday, NZPA reports.
Leon Birnie was the hero for the home side, converting a penalty in the 11th minute and scoring a 63rd-minute header to complete the comeback after Allan Pearce and Neil Sykes' first-half goals gave the visiting side a 2-1 lead at the break.
Auckland City and Manawatu now trail Waitakere by three points but have games in hand - Auckland two and Manawatu one.
Both clubs remain in second and third place respectively with 10 points.
A win for Waitakere United would have opened up a five-point lead in the race for the NZFC minor premiership.
In the capital, the 10 men of Wellington snatched a dramatic 2-1 win over Waikato FC.
