Frustrated Real coach Alvaro Arbeloa, meanwhile, highlighted a litany of shortcomings in his side's performance after their hopes of automatic qualification were dashed and they had to settle for a place in the two-legged playoffs.
For Mourinho, it was an emotional night at the Estadio da Luz, capped by an extraordinary 98th-minute header from Trubin that ensured Benfica snatched a last-16 spot on goal difference.
The Portuguese manager was visibly moved as he spoke to Movistar Plus after Benfica's stunning victory.
"It's normal for me to be emotional. I think it was deserved," Mourinho said, reflecting on the intensity of the contest and the dramatic finale.
"For Benfica, it's obviously incredible prestige to beat Real Madrid. The two clubs hadn't faced each other since the fantastic years, so many years ago. And now, for Benfica's prestige, for the players' prestige, it's something fantastic."
The teams last played each other in the European Cup in the quarter-finals in 1965, when Benfica went on to lose the final, and also met in the 1962 showpiece won 5-3 by the Portuguese.
Mourinho heaped praise on 24-year-old Trubin, whose header from a stoppage-time free kick sent the crowd into raptures.
"I knew we weren't through yet, that 3-2 wasn't enough, and we were lucky with a set piece," Mourinho said.
"Our goalkeeper Trubin, who is two metres tall, went into the box and scored a fantastic goal, a historic goal ... It felt like the stadium was going to collapse. Incredible."
In contrast, Real's Arbeloa was left to rue a poor display by his side that saw them lose a 1-0 lead and finish with nine men after Raul Asencio and Rodrygo were sent off in added time.
The defeat sends the 15-times Champions League winners into the playoff round, where they must attempt to salvage their European campaign.
"Of course we are far from happy. Quite the contrary," Arbeloa said. "In a match where we knew what was at stake, we simply didn't rise to the occasion.
"I'd like to tell you that it was just one thing that led to this defeat, but I think there were many aspects - adversity in duels, issues with the ball and without the ball. We were a long way from the version of ourselves that we should be."
Addressing the red cards, Arbeloa said tensions boiled over. "Sometimes these are situations where you can't control your emotions, knowing what was at stake. That's all there is to it."
For Mourinho, the victory was as much a boost for the club's stature as it was for their Champions League prospects.
Arbeloa must now prepare his side for the playoffs as he attempts to get Real's season back on track after former manager Xabi Alonso's sacking and the team being knocked out of the Spanish Cup last-16 by second-tier Albacete two weeks ago.