"It was always going to be a tough game," Athletic coach Jason King said.
"We knew that after last week and we had to fight hard then. Pretty disappointed not to get there, I think we did enough, but a couple of mistakes cost us, and they were our mistakes."
Buoyed by a strong showing last week Athletic absorbed some early pressure to take a fifth-minute lead when Quinn Mailman won a tussle with Marist keeper Dominic Semmens.
The keeper fumbled the ball on the ground under pressure from Mailman, who stretched to keep it in play and regained his footing to finish from a tight angle.
Marist survived a wave of Athletic attack over the next 20 minutes with the home side playing as good as they have all season - Jordan Candish, Peter Czerwonka and Scott Burney all creating work for Semmens.
The Marist equaliser came almost against the run of play and its real value to the visitors was that it killed some of Athletic's momentum.
Still, they got themselves back in front again when Burney found the goal in the 34th minute to have Marist chasing again.
But not for long.
Three Marist goals in nine minutes straddling the break proved too much for Athletic to haul in this time.
Hat-trick scorer Lee Rufer feasted on Athletic scraps to bring Marist level again before Robbie Yule gave the Manawatu side the lead before the break.
As they did last week, Athletic conceded in the opening minute of the second spell with Adam Cowan finding space to set up Rufer's second, leaving Athletic a massive task to rescue their cup campaign.
Athletic had come back from the same margin at the same point last week and there was a sense of déjà vu when Marist conceded an own goal six minutes later giving home fans hope.
Wanganui Athletic's Logan Hughes looks to get a cross away. Photo / Lewis Gardner
But Marist are too good to make a habit of giving up leads and their two-goal buffer was restored in the 55th minute by a strong Ludwig Zeoula strike from the edge of the box.
Athletic kept pressing and had chances, including several more from Candish who was unable to make one count and Ryan Holden who slid across goal to collect a volley at point blank but it was well blocked by Semmens.
With Athletic pressing Zeoula was able to find the open ground to provide the assist for Rufer's hat-trick goal and seal Marist's place in the cup's second round.
The loss also ends Athletic's unbeaten run at Wembley Park at 364 days – the last loss an extra time Chatham Cup loss to New Plymouth Rangers in 2017 – though their unbeaten home run in league football continues.
"Now I guess we'll have to just keep talking about the league like we did last year," King said.
"Unfortunately, couldn't get past round one again which is a bugger. I know the boys certainly believed they could do it but at the end of the day the score sheet says different.
"Do we need to look at stuff defensively? Maybe. But, I mean, it's the same people, same structure that we've done in other games, we just need to put more in at the other end.
"At the end of the day two of those we gave to them and the other two near the end was when we were pushing. We had some really good opportunities and we just couldn't finish them.
"That's cup football, you've got to throw the kitchen sink at it and if you don't you're not playing the right game."
While Athletic check out of the cup at the same point as last year, in a way, they've done better having been drawn to play a preliminary round which they won 3-1 against Rangers.
Athletic can now refocus on the Federation League where they sit in fourth as they head to Palmerston North for the next two weeks to play Red Sox and North End to cap off the first round.
