With Dan Sheehan rested before next week's match against New Zealand in Auckland, Tadhg Beirne stepped up to captain Ireland for the first time as one of nine changes to the line-up from last week's 33-31 win over Australia in Sydney.
But while Ireland scored some well-worked tries, Beirne was frustrated by his side's set-piece frailties, with both Japan tries coming after Irish line-out mistakes.
"We just kept shooting ourselves in the foot a little bit, whether it was discipline or leaving them access, especially in the second half, we were kind of camped on our own line," said Beirne.
"There were some errors in the game, especially around set-piece that fed their energy and gave them opportunities to attack, but credit to the lads, we fought hard to keep them out at times and get the win."
The performance of Jansen - one of four debutants in the Ireland team alongside Billy Bohan, Sam Illo and Bryn Ward - was a positive for Farrell.
The New Zealand-born back row was denied a try in the first half when he was stopped by Tiennan Costley's superb tackle, but the 27-year-old touched down in the second half to ease the pressure on Ireland.
Jansen said it was a "dream come true" to win on his Test bow - and his display clearly left an impression on his coach.
"The way Sean Jansen actually attacked the game as a debutant was there as a learning for everyone," Farrell said.
"To be able to get the man of the match and play like he did first up is a massive credit to him and it's a great learning for others coming in."

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