On-loan Fulham striker Trotta, 20, insisted on taking the last-minute spot-kick which would have fired the Bees to automatic promotion on the final day of the season ahead of skipper and designated penalty-taker Kevin O'Connor.
But he crashed his effort against the crossbar and Doncaster broke away to score at the other end and seal the League One title.
However, Trotta put in a fine performance as Brentford won their play-off semi-final against Swindon on penalties following a thrilling 3-3 draw on Monday.
They face Yeovil in the final at Wembley a week on Sunday and Trotta admitted: "You feel very disappointed and you want to give something back to the team and the fans.
"You have to give everything you've got and fight for your life and the team did the same and that's why we won.
"We've got another game to go. We've got the final. I think the lads put in a great effort. They've done unbelievably well. As a team, I think they're great.
"I think the fans have been great. Even after last Saturday they've been great in supporting me and the team. They were behind us and pushed us up for one more. Wembley will be an unforgettable experience."