It is a rarity that the stellar fly-half is ever replaced but he endured a catastrophic evening at Twickenham.
Farrell, 27, gifted Scotland two tries via a charged-down kick and intercept pass as the hosts somehow threw away a 31-0 lead to trail 38-31 heading into injury-time.
He was also lucky to stay on following a shoulder charge with Jones replacing him soon after in the 70th minute.
Ironically, his replacement George Ford stepped up to save England’s blushes scoring the converted try in the final play.
“We just needed a change, and someone to change the momentum of the game,” explained Jones.
“I thought Sladey and Manu (Tuilagi) both still had enough in them to keep on, so it became a decision on whether to replace Owen; we thought it was the best decision for the team at that stage.
“Owen lost a bit of his edge. He was just a little bit off his best and George Ford has been in exceptional form this week.”
Farrell conceded England gifted Scotland the momentum swing – “me more than anyone” – but coach Jones maintained: “It’s always a team loss.
“You never lose because of one player. He’s the world’s hardest taskmaster. He’ll be disappointed with his game.”
Asked if it was a problem his captain struggling mentally, Jones replied: “He’s a young captain and he’s developing really nicely. Like any young captain it takes time; you don’t put a C next to someone’s name and they learn every lesson on how to manage a game.”