"A linesman overruling a ref's decision, I think, will be one of the only times you'll ever see it happen in a football game," he said.
Appointed referee Chris Kerr had pulled up injured shortly after halftime.
Debutant Ethan Galbraith was the game's only scorer in the premiership, which resumed at the weekend after the Christmas break.
Galbraith, who made a name for himself when he scored the winner for Birkenhead United in last year's Chatham Cup final, slotted home from close range in the 65th minute.
The hosts had to rally when they lost goalkeeper Pirmin Strasser in the 39th minute to a suspected fractured cheekbone but replacement Liam Anderson showed he was more than able.
The No 2 keeper made several saves to thwart the attacking efforts of Bay striker Saul Halpin, in particular, to maintain a clean sheet.
Chettleburgh said Anderson played out of his skin, making a rash of saves.
"He made a really good save and I don't know how he did it off a Saul shot in the second half."
Chettleburgh singled out wing back Kohei Matsumoto for his surging runs down the flank.
"He did some good things for us and was always up and down," he said although he was loath to single anyone else out for a tidy effort.
Rookie striker Jorge Akers got about 15 minutes off the bench.
"Jorge did well and held his own. He worked hard and put in one fantastic ball, which arguably we should have scored off but things weren't really going our way."
Bay United were hoping to make a determined start to 2017 after stumbling away to Hamilton Wanderers before Christmas but it was not to be.
"We're coming and back home so we're hoping for a good three points this weekend," Chettleburgh said of the 2pm kick off against Eastern Suburbs on Sunday at Bluewater Stadium.
Bay United were without skipper Finlay Milne marshalling the Beefeaters from his vantage point at centreback and fellow defender Sean Liddicoat, both serving a match suspension for accumulating yellow cards.
"It's always difficult when you're missing two players from your starting eleven, not to take away from the players who came in and played because I think they did a good job but especially with Fin's leadership out there on the field," said Chettleburgh.
"We're always going to miss that especially when we're going away from home to play against one of the Auckland teams."
It was an ill-tempered match in the opening round loss to Bay United in Napier on October 24 but Waitakere United exacted revenge when they pipped the visitors in the return fixture.
Chettleburgh said there weren't any recriminations over the previous encounter.
"Nah, not really. We just tried to play our game and see where it would take so there were no really afters or anything like that and it was played in good spirit, I guess."
In the season opener at Bluewater Stadium Park Island, Waitakere had lost 3-1 but lodged a protest with the New Zealand Football competition authorities, claiming the Brett Angell-coached Bay had fielded too many foreign players.
However, that complaint was investigated and thrown out.
"They played a particularly different style to what they normally play to us. They were quite direct and they had some big guys up front who they tried to feed the ball to and feed off the second-phase balls so that turned it in to a battle," said Chettleburgh, admitting it worked in their favour. The burly blokes were Galbraith and Dylan Stansfield.
"Obviously we're disappointed in not getting anything out of the game. Any time you lose points you can't be happy."
Skipper Chettleburgh bemoaned missed chances that would have gone in to the goalmouth any other day.
Sunday's defeat saw Bay United slip to seventh on the premiership table with 13 points, after four wins and five losses.
However, it's not panic stations as they are only four points off reeling back the other six teams above them.
