England international Farrell missed the quarter-final victory over Glasgow Warriors to attend the birth of his first child and he contributed 22 points on his European return.
Michael Rhodes scored the first try of the game as Sarries added 13 unanswered points at the start of the second half to storm to victory, with defending champion Leinster or Top 14 leader Toulouse awaiting in the final at St James' Park.
Munster responded through Darren Sweetnam but Billy Vunipola, who had been booed during the match after showing support to Israel Folau in the wake of the Australia international's latest controversial social media posts, ensured the Irish province suffered defeat in a seventh straight European Champions Cup semi-final outing.
Farrell took two minutes to get off the mark from the tee but after he skewed an attempted drop goal wide, Tyler Bleyendaal — starting at five-eighth because ofJoey Carbery's hamstring injury — restored parity.
A pair of Farrell penalties created some separation between the teams until Bleyendaal and Conor Murray restored parity, although Farrell gave Saracens the half-time advantage with the final kick of the first half.
Brad Barritt was replaced by Nick Tompkins for the second period and Sarries were ahead within five minutes of the restart, Rhodes darting through a gap in the Munster defence and Farrell adding the extras.
The Premiership side did brilliantly to hold up Chris Farrell on the line before losing control of the ball at the scrum and Murray got it moving for Sweetnam to touch down in the corner.
Saracens' Farrell missed from the tee for the first time in the 67th minute but they moved out of reach when Vunipola touched down at the end of a sustained spell of pressure.
Vincent Koch was sent to the sin bin in the 77th minute for an illegal clear out but Mark McCall's side never looked like losing its place in the final despite finishing a man light.