The hosts prevailed 29-14 on Friday in Sydney, but only after trailing 14-12 at halftime and being forced off with just 11 minutes remaining for 40 minutes due to nearby lightning strikes.
The weather forced the Duke and Duchess of Sussex, Harry and Meghan, in the company of rugby royalty including John Eales, out of their seats in the second half.
Victory broke a three-game losing streak to Pasifika and improved the Waratahs to 4-4 and in sight of the top six ahead of a crunch Super Round clash with the Crusaders in Christchurch next Friday.
Waratahs coach Dan McKellar revealed they had planned for the possibility of a lightning delay and was pleased with how they handled it.
"If you're helter-skelter and off the cuff, who knows what happens in that last 10 minutes," he said, while again lamenting too many turnovers.
"It (the win) keeps us in the hunt; we just have to keep knocking on the door."
Pasifika, whose ownership on Wednesday confirmed it would be unviable to continue funding the outfit beyond this year, started well and had their chances to build a lead early in the second half.
But twice they knocked on close to the line and then piggy-backed the hosts towards their own line with scrum ill-discipline and line-out errors.
Eventually, after some sloppy unforced errors of their own, the Waratahs pounced.
Isaac Kailea crossed after repeated, pounding efforts from close range, then Sid Harvey had his second to make it 22-14.
The fullback didn't get a chance to convert his own try with players forced off due to the electrical storm and taken into the changerooms.
He hooked it past the upright on resumption but made a huge play to knock a ball loose just as Pasifika's Solomon Alaimalo had broken clear.
Semisi Tupou Ta'eiloa's own hand then denied him a try near the posts, the flanker held up in goal with five minutes to play.
The Waratahs controlled possession for the final minutes and Folau Fainga'a's rolling-maul try secured the extra point on the buzzer.
Earlier, Pasifika halfback Melani Matavao caused all sorts of problems in the first half with two tries from quick taps around the ruck.
The crafty No.9 played it perfectly, knocking on deliberately after earning the penalty before running through an offside Waratahs defence.
Tristan Reilly and Harvey, athletically diving into the corner, both scored to keep the hosts close at the break.
Moana (1-8) had lost their past seven games, conceding an average of 48.3 points in those losses, but arrived in Sydney with plenty to prove.
Licence-holders New Zealand Rugby are hopeful fresh investment can save the Auckland-based franchise, designed to represent Tongan, Samoan and Cook Islands.
But after poor results, a lack of public and commercial support and just two games in five seasons played in either Samoa or Tonga, plans are being formulated for a 10-team competition without them for 2027.
Coach and former All Blacks great Tana Umaga was proud of his side's "get on with it" attitude after being told of the club's plight.
"We talk a lot about why we do it and those are the first things that come to mind ... our families, our friends and fans," he said.
"Those things galvanise you to try to get on and keep doing what we love doing.
"There's a glimmer of hope for us and that's what we have to look forward to."
