Sportal.co.nz 25.Mar.2013Getty Images
Schalk Brits and Will Fraser crossed over, while Owen Fraser kicked 17 points as Saracens maintained their unbeaten record at Allianz Park.
The early stages were an even affair with both teams exchanging penalty conversions through Farrell and Nick Evans, who kicked the visitors to a 6-3 lead inside 13 minutes.
Saracens began to take a stranglehold of the match from that point, with Farrell adding three more penalties in the opening half.
Brits scored the game's first try after 26 minutes, bustling his way through a number of Harlequins defenders to give Saracens a 17-9 lead heading into the interval.
Harlequins quickly cut the lead to five points after half-time, Evans slotting home a penalty.
However, the hosts restored their lead through Fraser, who finished off a well executed attack by crossing over.
Farrell stepped up to convert and give Saracens a commanding 24-12 advantage before adding another penalty.
Harlequins pressed for a try following Chris Ashton's dismissal to the sin binned but the visitors were unable to make the most of their numerical advantage.