Wanganui made a forward pass from a lineout play with 90 seconds left, and that was the ball game.
"The first try was really good. The second try, decision making - we didn't mark up on the blindside," said co-coach Jason Hamlin.
Turning to face the breeze, his team needed to be 6-8 points further ahead but they were unable to sustain pressure due to over-reaching and getting pinged.
"That's really the story of the game for us - it let us down. We sort of piggy-backed them up the field in the first half.
"A couple of poor decisions that put ourselves under pressure when we didn't need to.
"Very much the same [as Poverty Bay], our skill execution wasn't as good as we like it.
"We could have cleared and made life a hell of a lot easier, but we didn't. We were one breakdown away from putting the points on."
The co-coach singled out No8 Bryn Hudson for a strong match against the big South Canterbury pack, while returning lock Sokonaia Kalou was also strong until being replaced late in the second half.
Adding to the team's injury concerns is winger Simon Dibben, who will miss at least a week after hurting his hamstring.
Heading back to Canterbury this coming Saturday for the now crucial game in Ashburton, Hamlin said it was time to "put the pressure" on certain players to tidy up the areas where it has been going wrong - given this potential loss to the now table-topping South Cantabrians had loomed after two previously scratchy wins.
"A bit of execution and discipline, and that's the consistent thing for us."
Hooker and captain Roman Tutauha agreed.
"We were our own worst enemies. We put ourselves in good positions but our penalty count let them off."
Having repeated conferences with the referee, Tutauha said the issues were rushing up at the offside line, and then a lack of discipline at the breakdown.
"Hands off the ball - we slipped into that trap.
"We've been saying each week, 'we learn from this one'.
"But this week, it's really learn. Same circumstances [against Mid Canterbury], we really got to turn up."
Clare opened Wanganui's account with his first penalty inside the opening ten minutes, then second-five Timoci Seruwalu crossed for his fifth try in four games for 8-0.
Despite dominating territory, Wanganui could only add another Clare three-pointer, then South Canterbury hooker Marac Beckham lifted his team's spirits with a converted try with six minutes left in the half.
Clare replied quickly with another penalty, and then when kicking into the breeze just after the break he struck the ball low and hard for 17-7.
But Canterbury teams will never fade away and after Leatigago carved Wanganui up, it was the home side who were turning gifted territory into opportunity.
"It's always a hard ask for anyone to come here," said Tutauha.
"They turn up another level and turn up for 80."
It was the end of an undefeated Heartland run going back to the 30-28 injury time loss to Mid Canterbury at Cooks Gardens on August 29, 2015.
South Canterbury moved to the top of the Heartland rankings, but thanks to a tight table where fellow unbeaten sides Buller and Horowhenua Kapiti lost away games this weekend, Wanganui only slipped back to second place.
South Canterbury 21 (Marac Beckham, Kalavini Leatigago, Brad Hemopo tries; Willie Wright 3 con) Wanganui 17 (Timoci Seruwalu try; Craig Clare 4 pen). HT: 14-7 Wanganui.