The second-tier outfit produced a memorable upset by eliminating top-flight side Sekhukhune United, edging them 3–2 in a penalty shoot-out after the contest finished 2–2 following extra time.
The Stallions came into the match recovering from a narrow 1–0 loss to Midlands Wanderers that ended their five-game unbeaten streak, and Pupuma says the result against a Premiership opponent has helped restore belief within the squad.
"We always viewed this game, especially after we lost last week, as a sort-of motivational win if we could get it, so I think we achieved that," said Pupuma.
"It's going to lift the spirit way up in the camp going to Cape Town and then Mpumalanga, and about getting into the semifinal, who wouldn't be happy going into a semifinal of any cup?"
Next up for second-placed Milford is a fixture against third-placed Cape Town City, with only a point separating the two sides on the MFC log standings.
The coach now faces the challenge of balancing their Nedbank Cup campaign with the push for league success – a situation he admits can be difficult to manage.
"How then do you tell players not to commit and not to give their all in a game? You can't say, 'You know what, let's just show up today, we don't have to win this, we have to win the league,' and so on," he added.
"So, unfortunately in the Milford setup, every game is important – we play to win every game and what happens afterwards, we address it when it happens."
Milford will find out who they face in the Nedbank Cup semifinal draw on Monday night.