The goal, deflected past keeper Adam Highfield, was a body blow to coach Malcolm Fleming's under-strength side which had looked lively until then.
Wellington went on to dominate the half, with Scotsman John Sutherland scoring two goals that were worthy of awards by themselves.
Sutherland's best was a flashing volley that flew past Highfield, who actually had a fine match.
The big keeper tipped a couple of blazing shots over his crossbar, and punched away a couple of swerving corners that spelled danger.
Wellington coach Charlie Howe was in charge with Stu Jacobs away in Sydney, and the stand-in was delighted with his team's performance.
"It's a pretty young Wellington side, mostly from our area, and they played smart football today, keeping the ball well, and setting up lots of attacks," he said.
It was Wellington's Karl Whalen's 100th national league appearance, and the team captain turned on a five-star performance, along with young centreback Pomare Te Anau, and Mike Eagar.
Otago's best were keeper Highfield, Andy Coburn in the unusual position of centreback, and Nathan Knox, whose skill and energy set benchmarks for Otago.
Tom Connor also had an impressive match at right fullback, a position he is making his own after years playing midfield.
Left fullback Tristan Prattley had a typically sound game, providingsome searching crosses that tested Wellington's defence.
But understandably with so many changes, the team shape was far from watertight and allowed the slick Wellington side to penetrate with ease in the first half.
Coach Fleming said: "We played much better in the second half, did not lose as much possession, and in fact as we brought on substitutes like Harley Rodecka, the team produced a surge of energy that had Wellington on the back foot."
Otago's best chances fell to Ant Hancock, who forced a top reflex save from Wellington keeper Phil Imray, and when the big keeper could only block the ball, Hancock shot the rebound just over the visitors' crossbar.
So it's back to square one for the Otago squad which travels next week to bottom ASB Premiership club Manawatu, beaten 3-nil by Waikato this week.
