The Spaniard was targeted by Boro for some heavy tackles, but he got his revenge with two classy goals on 26 and 67 minutes.
The match was then effectively over as a contest as Gareth Southgate's side looked unsure as to their game-plan and, even when they fell behind, had little attacking ambition.
The first real opportunity, in a game that began quietly, came on eight minutes when Fabregas played a slide-rule pass into the path of Theo Walcott. However, the young Englishman took one touch too many and Robert Huth was able to get back to make the tackle.
The opening goal was worth waiting for though and was as good a team goal as will be scored all season.
The move, which was played at lightning speed, began with Andrey Arshavin in Arsenal's half. The Russian curled a pass to Nicklas Bendtner who flicked it with the back of his heel to Fabregas.
He in turn delivered a diagonal ball to Arshavin who had gone on a lung-busting run down the left flank. The diminutive Russian then pulled a pass back to pick out Fabregas who fired the ball from the edge of the area low and hard into the right side of the net.
Had it not been for Walcott dwelling too long on the ball again, the Gunners would have doubled their lead in the 33rd minute.
The England winger was fed by the energetic Samir Nasri but, instead of instantly crossing for the waiting Bendtner, he took it on to the by-line and, his cross flashed across the goal untouched.
Boro's first shot of note came two minutes before half-time when Stewart Downing's 25-yard drive from the right was gathered at the second attempt by the fit-again Manuel Almunia.
The Gunners began the second half at a high tempo after Johan Djourou had come on for Mikael Silvestre.
Brad Jones was forced to make a smart close-range save to deny Walcott after the Gunner had been found by Emmanuel Eboue who had gone unchecked on a cavalier run down the right flank.
Arsenal doubled their lead midway through the second half when Fabregas latched on to an incisive throughball from Kolo Toure. The Spaniard rounded the oncoming Jones before rolling the ball into an empty net.
Jones made a good save from Bendtner five minutes later, but the Gunners seemed to take their foot off the accelerator after scoring the second goal.
At the other end Southgate's side looked distinctly impotent and so there was little fear of Arsenal being punished.
The forthcoming Champions League game against Manchester United was clearly on the Arsenal players' minds as they looked to conserve their energy.
Sir Alex Ferguson was watching in the Emirates Stadium stands, but there was little for the United boss to learn after Fabregas's second strike, particularly after the Spaniard and Walcott were replaced immediately after that second goal.
Abou Diaby showed a good turn and shot in the last minute of the game, but that was the extent of the excitement and Boro, on this afternoon's tame performance, look likely to be relegated.