Whanganui went ahead in the 22nd minute and led at halftime.
Thistle equalised through Jimmy Somerton – now the league’s equal-second top marksman with 11 goals – in the 52nd minute.
Five minutes later, Whanganui regained the lead and in the 64th minute, they scored again.
“For the last 20 minutes, it was all us,” Cramer said.
“They just parked the bus. Sam Hotas had a shot cleared off the line, we went close in goalmouth scrambles, their goalkeeper made an outstanding save.
“No one played badly.”
He was confident that a full-strength Thistle side – as at the middle of last week – would have provided the playing depth to win the match.
He said left-winger Ruben Garcia – having his first Federation League start – had a great game, and right-back Te Kani Wirepa-Hei gave an outstanding defensive display, particularly in the second half.
Travis White and Somerton linked up well, and Hotas also created problems for the Whanganui defence.
Thistle lined up with Hugo Lodewyk in goal, Kaden Manderson and Wirepa-Hei in the fullback positions, and Junior Jimmy and Cory Thomson as double centrebacks.
The central midfield trio comprised David Salmon, Isaac Bush and White, with Garcia and Hotas out wide. Somerton was the attack spearhead. Thistle remain in sixth position in the nine-team league.
The top three teams gain automatic inclusion in the Central League second division being reintroduced next year. Teams placed fourth to seventh will play off against Capital Premier and Capital 1 teams.
The higher Thistle can finish in the Federation League, the lower will be the ranking of the team they meet in the playoffs.
In other Central Federation League fixtures at the weekend, Palmerston North Marist beat Peringa United 7-0, Palmerston North United beat New Plymouth Rangers 2-1 and FC Western were awarded a 3-0 win for the default by Havelock North Wanderers. Taradale had the bye.
Points: Palmerston North United, 30 points from 13 games; Palmerston North Marist, 30 from 14; FC Western, 25 from 13; Havelock North Wanderers, 22 from 13; Taradale, 21 from 13; Gisborne Thistle, 15 from 12; New Plymouth Rangers, 13 from 13; Whanganui Athletic, 10 from 13; and Peringa United, 7 from 14.