Spurs booked their place in the final of the competition thanks to a last-gasp winner from Lucas Moura.
The Brazilian completed his hat-trick to setup a Champions League final clash with Liverpool.
And Fabregas took to social media to praise Tottenham and their boss Mauricio Pochettino.
He tweeted: “Credit where it’s due. What a come back from Spurs. What a coach Pochettino is.”
Arsenal fans reacted angrily towards their former midfielder’s comments.
One tweeted: “Delete this now!!! I love u cesc but that’s just not on.”
Another simply added: “Snake.”
“Okay this is not Cesc. What have you done to Cesc?,” a third said.
A fourth exclaimed: “This can’t be happening.”
Fabregas left Arsenal for Barcelona in 2011 before he returned to the Premier League with Chelsea.
The Spaniard is now playing for French outfit Monaco in the twilight of his career.
Pochettino hailed his side’s victory in Amsterdam and was emotional at the end of the sensational comeback.
“To get the club to the final of the Champions League… I think is very close to a miracle,” he said
“No one believed in us from the beginning of the season.
“We are so close to the top four and have the opportunity in Madrid to play the final against Liverpool.”
Tottenham finish their Premier League campaign on Sunday with a home clash against Everton (3pm).