"So when they saw we played the passing game, they would just hammer it down the other end, making our guys chase it."
Top goalscorer Ryan Gray got a green card in the 42nd minute, while Ronan Spence was given a yellow with 60 seconds left.
At 0-0, it went to the best-of-five shootout and Pratt was able to keep one more out than Wanganui's Tim Reardon.
Spence said the team took it hard because while they received silver medals, it felt as though they had lost without being truly beaten.
"It was pretty disappointing. The boys played really well."
Six of the senior players will now move on to under-18 level, leaving about 10 eligible for next year's national championships.
That will be held in Wellington and after fifth in 2013 and runnerup this year, Spence was hopeful that Wanganui would be able to "finish the job" in2015.