The Warriors moved off the bottom of the National Rugby League ladder, at least temporarily, with only their fifth win for the season.
New Zealand was in control of the game at Ericsson Stadium by halftime, leading 18-0.
The Eels fought back in the second half but couldn't reel in the deficit, going down three tries to two in miserable conditions at Ericsson Stadium.
The Warriors will stay off the bottom of the ladder as long as the second-last Manly Sea Eagles lose to the Bulldogs at Brookvale Oval on Sunday.
Smith claimed the Warriors set out to waste time during the game.
"I thought they played aggressively and they definitely had a plan to play the game and extend, shall I say, the periods when the ball wasn't in play to an exceedingly long time," he said.
Smith, who notched up his 200th game in charge at the Eels, said referee Steve Clark didn't seem to be able to stop the time wasting.
"Maybe the rules don't provide for it, for him to be able to do something about that," he said.
"But the breaks in play, the goal line drop outs, the feigning of injury, the walking to scrums, all of that stuff just made the game quite painful I thought."
Warriors coach Tony Kemp shrugged off Smith's comments.
Asked if it was part of the Warriors' game plan, Kemp said: "Not at all, I don't know where he got that from."
Smith and fullback Wade McKinnon said the Eels weren't prepared for the wet and windy Auckland conditions.
"I thought if we had taken some chances a little better that we may have snatched the game, but it was always going to be a tough game for either team to win tonight I thought," Smith said.
It took 53 minutes before the Eels finally troubled the scorers through English halfback Chris Thorman who was slotted into pivot off the bench just before kick-off by Smith.
Winger Matt Petersen put the Eels back in with a chance with 15 minutes left on the clock, running in their second try but Michael Witt missed the conversion attempt.
The Warriors' three tries all came during the first half, which Jones agreed was probably their best 40 minute performance this year.
After tries from centres Jerome Ropati and Clinton Toopi, Jones intercepted a Thorman pass and sprinted 55 metres to score his side's third try in the 35th minute.
The Eels - minus second rower Nathan Hindmarsh who is in camp with the NSW State of Origin team - had plenty of scoring chances, only to be thwarted by the Warriors or by their own misfortune.
The Warriors also suffered as the conditions worsened in the last 40 minutes, with both teams dropping the ball during what Jones described as an ugly second half.
Warriors winger Henry Fa'afili was put on report for a high tackle on Petersen and second rower Epalahame Lauaki came off after taking a knock to the arm.