TV replays showed Fletcher touched the ball before he sent Fabregas flying. But the Euro 2008 official decided the Scot had denied a clear goal-scoring opportunity and sent Fletcher off.
As there is no appeals procedure, Fletcher will miss the final against either Chelsea or Barcelona in Rome on May 27.
"I am so sorry for Darren Fletcher," said Evra.
"The real big bad news about all this is Darren not being able to play in Rome.
"I am very, very frustrated and disappointed for him and his family."
After picking up a booking in the first leg, Evra knew another would see him miss out as well.
He avoided such an unhappy conclusion last night, although he was thankful Ferguson decided to take him off once Manchester United had scored their third in a remarkable 3-1 victory over Arsenal at the Emirates Stadium.
"I played with a lot of pain in my stomach worrying about missing the final," he said.
"I said to the boss if we score a third goal I want to come off because I just cannot miss that match.
"It was a real fear for me. In the hotel before the game and all during the previous week I was thinking about that yellow card.
"I believed United would get to the final but I wasn't sure I would. It was very painful to play with that on your mind."
Now Fletcher can only wait and hope, although Ferguson is not entirely without that.
"Darren is one of the most honest players in the game and to miss the final is a tragedy. He was distraught," said the Scot of his fellow countryman.
"In respect to the referee in this situation he might look at it himself without anyone asking him.
"We shouldn't ask him. He's competent and fair enough to look at it himself possibly. Apparently, you can't appeal and if that's the case it's disappointing for the boy."
In the end, Evra conquered his own anxiety by telling himself to accept what fate had in store.
The outcome was certainly more to his liking than opposite number Kieran Gibbs, whose untimely slip gifted Park Ji-sung his opener.
Cristiano Ronaldo's stunning 40-yard free-kick effectively finished the tie after 11 minutes, the world player of the year adding a brilliant third after half-time to which Arsenal's only response was Robin van Persie's penalty.
The outcome leaves United one win away from becoming the first team to retain the European Cup since it was rebranded as the Champions League in 1992.
With only seven points needed to clinch another Premier League title and the Carling Cup and Club World Cup already in the bag, this is shaping up to be the best season in the club's history.
Not that Evra is getting carried away just yet.
"It is too early to say if we are the best Manchester United side," he said.
"If we win the final then we will have to see."