Farrell dropped the ball over the line while attempting to touch down for Saracens' second score and it almost came back to haunt the visitors as Toulouse scored two late tries.
But two late penalties from Farrell helped Saracens to end Toulouse's unbeaten record at home this season and confirm the Aviva Premiership side as one of the favourites to win this year's competition.
Former England international Charlie Hodgson was controlling things for the visitors early on with some lovely kicking from hand.
He put Saracens in front after just minutes with a penalty after good work by his forwards.
Hodgson was putting the Premiership side into excellent positions with his boot and made the most of a visit into the Toulouse half with a drop goal to nudge them further in front.
The battle up front was dominating the contest early on and both sides were finding it difficult to make serious inroads into the opposition's 22.
Saracens were well on top for much of the opening half an hour and a second penalty from Hodgson gave them a healthy lead heading towards the half-time break.
But with three minutes left of the opening half Toulouse stung the visitors with a try after Saracens wing Duncan Taylor failed to deal with Luke McAlister's kick over the top and the former New Zealand international was able to collect and crash over from close range.
It was the first time Toulouse had been in Saracen's 22 but Toby Flood adding the conversion they went into the interval just two points behind.
Saracen's Owen Farrell was in the thick of the action at Toulouse
Image credit: PA Sport
Farrell replaced Hodgson at half-time and was immediately on the score sheet with a penalty.
Saracens then scored a superb try when Alex Goode launched a counter-attack from his own half and found Ben Spence, he chipped over the top with the outside of this boot before collecting his own kick to score.
The visitors should have got a second try when Jamie George's burst downfield took them into the Toulouse 22 and after several phases Farrell went through a gap only to spill the ball forward before he could touch down.
Farrell made up for the error shortly afterwards when he produced a try-saving tackle to stop Yacouba Camara going over but it was not long before McAlister got his second score of the game to bring Toulouse back into the contest.
Spencer then spilled another good chance for Saracens close to the Toulouse line after a break from Duncan Taylor.
With 10 minutes to go Toulouse got their third try of the afternoon when Maxime Medard did well out wide to find Paul Perez on his inside and the wing did a superb job to control the ball with his feet and go over.
But two Farrell penalties in the final seven minutes secured the win for Saracens.