Farrell stars for Saracens against Quins before injury strikes
The match between the London clubs had been billed as a Farrell v Smith showdown and while each had their moments at the home of Premier League football club Tottenham, it was Farrell, with the benefit of playing behind the stronger pack, who had the best of it.
But Farrell's match ended 10 minutes before full time when he rolled his left ankle while making a tackle close to Saracens' posts.
His injury took some of the shine off a win that guaranteed Saracens a home semi-final tie in the title-deciding play-offs.
Saracens' Billy Vunipola took man of the match honours after a display where he got the better of Harlequins counterpart Alex Dombrandt, the current England No. 8, in front of more than 55,000 fans.
Dombrandt opened the scoring inside 90 seconds when he sold a fine dummy before going over for a fine try.
Saracens, however, hit back as Alex Lozowski scored between the posts before helping create his side's second try for Wales' Nick Tompkins.
Harlequins scrum-half Danny Care was sin-binned for interfering at the ruck and Farrell's penalty meant Saracens led 17-7.
Quins hit back early in the second half with two tries from winger Cadan Murley but centre Luke Northmore was sin-binned for catching Farrell in the throat and in the next play Saracens's Maro Itoje was driven over for a try from a line-out.
Joe Marler's try kept Quins in the hunt but Saracens, last season's losing finalists, retained control to remain top of the table.
Earlier, South Africa's Rugby World Cup-winning fly-half Handre Pollard scored 19 points, including a try, and Argentina's Julian Montoya crossed twice as champions Leicester maintained their semi-final push with a 46-24 win over Bristol.