Fabian, a surprise starter after Pedri dropped to the bench, opened the scoring before Merino came on after 86 minutes and struck two minutes later, pouncing when substitute goalkeeper Senne Lammens failed to hold Pau Cubarsi's low strike.
It was the third time Merino had scored a knockout winner as a substitute under De la Fuente, after his late extra-time goal against hosts Germany in the Euro 2024 quarter-finals and his late strike versus Portugal in the last 16 at this World Cup.
"It's unfair that Mikel doesn't play from the start, but it would also be unfair if someone else were left out," de la Fuente told reporters.
"Only 11 can play, and they understand that - the role they have to play at any given moment. When they take to the pitch, they know what they have to do; that's why it's a pleasure to be their manager."
De la Fuente stressed that European champions Spain's run to the last four was built on collective responsibility rather than individual roles.
"What matters is the team," he said. "It doesn't matter who starts the match. Everyone is important, even those who haven't played."
Asked how he keeps players content despite fierce competition for places, De la Fuente praised their maturity and professionalism.
"One of our strengths as a team is that we have not only the best players in the world – which they are – but also the best people, people who make it easier for everyone to get on together," De la Fuente said.
"So we shouldn't be surprised that they understand their roles, because I believe this is possible in any field, in any profession. It's on the basis of respect that we build everything, and this national team is also an example of that."
Spain face tournament favourites France on Tuesday for a place in the final, with De la Fuente expecting a demanding contest.
"France have already shown some extraordinary, exceptional potential, and so have we," he said. "The match is wide open; it will call for fresh, energetic players ... but now that we're here, we're going to give it our all."