Head coach Richie Murphy says he is “bitterly disappointed” as Munster scored a last-gasp try to inflict a fifth defeat in a row on 14-man Ulster.
Ulster took the lead through prop Tom O’Toole, who was then shown a red card after Farrell scored the first of his three tries.
Farrell struck again after the restart, but Harry Sheridan hit back for the 14 men.
However, after Shane Daly and James McNabney exchanged tries, Farrell had the decisive say with the final play to give Munster 22-19 win in Belfast.
“I’m bitterly disappointed but absolutely proud of the effort and commitment that the lads put in,” said Murphy.
“I thought we found a way of getting back into the game. I’m incredibly proud of the lads’ commitment and performance, but we just need to be better in the really big moments.”
After O’Toole scored the opening try, the prop was sent off after referee Ben Whitehouse deemed he had fallen on the leg of centre Alex Nankivell at a ruck 10 minutes before half-time.
Murphy said it was a “tough” call but was pleased with how his side responded.
“Obviously the red card is a big moment in the game,” he added.
“It’s a tough red card because he is through the gate and makes contact square on. He’s not through the side, but as he falls backwards his leg comes out and Tom falls on it.
“I can kind of understand that, but it is difficult because it’s not an illegal act at the start.”