South Africa demolished Afghanistan by nine wickets to saunter into the final, where they will face India or holders England.
Afghanistan were bowled out for 56 off 11.5 overs after they chose to bat at the Brian Lara Stadium in Trinidad.
Trott conceded that his players had struggled to handle the pressure of a maiden World Cup semi-final, but he was still "very proud" of the team.
"A lot to process really emotionally, physically, so all new territory for the guys and it all plays its part," said Trott, a former England batsman who was born in South Africa, admitting his side had been "outplayed".
"I'm sure the guys hopefully learn from this experience," he said.
"(Learn) what it takes to play international cricket and play against a bowling side like South Africa on a pitch that's perhaps not conducive to high-scoring.
"We've found ways of winning games, we just couldn't find a way today," he said, adding that despite surpassing all expectations by reaching the last four, his side were left crestfallen.
"Obviously it hurts at the moment," said Trott.
"We arrived to the ground in high spirits ready to take on a strong South African side and make sure we gave a good account of ourselves.
"I feel like we haven't done that today so that's the most disappointing thing.
"I'm very proud of the guys. This one performance doesn't necessarily define the tournament."
Trott said Afghanistan's World Cup run, which included beating New Zealand, Australia and Bangladesh in a nerve-shredding win to reach the semi-finals, had been "a great ride".
The team provided rare moments of widespread celebration back home in a country ravaged by four decades of war and beleaguered by economic, humanitarian and political crises.
"I hope that we've inspired young kids to pick up a bat and a ball and play cricket, and want to play for their nation and hopefully that everybody's proud of the side," said Trott.
