Captain Farrell watched from the stands in Dublin on Saturday as England slipped to a meek loss compounded by the second-half red card of Saracens team-mate Vunipola for ploughing into the head of Andrew Porter.
Influential fly-half Farrell was free to feature in the warm-up game but was ultimately left out following World Rugby's appeal against the decision to overturn the red card he received in last weekend's win over Wales.
With England's World Cup opener against Argentina on September 9 fast approaching, Borthwick faces potentially being without two of his key men through suspension for the start of the tournament in France.
He was tight-lipped on Vunipola's tackle, but is eager for matters to be concluded quickly on the back of the disruption already caused by the ongoing Farrell saga.
"I'm not going to comment upon the incident specifically because it goes into a disciplinary process this coming week," said Borthwick.
"Probably as every England fan, I feel disappointment in the game today and I said beforehand we want 15 players on the pitch for 80 minutes of every game.
"You're playing the number one ranked side in the world in their stadium and to go to 14 men it becomes a very difficult task at that point in time
"Hopefully we will find a conclusion on both matters this week and it won't go into another week. Once I have all the facts, I will deal with them.
"We talked about the way this Test week was disrupted (by the Farrell situation) and I need to adapt throughout the week. It's another challenge that's been thrown at us."
England offered little at the Aviva Stadium, even before falling a man down when Vunipola's 53rd-minute sin-binning was upgraded to a red on review.
Tries from centres Bundee Aki and Garry Ringrose gave Ireland control at the break, before scores from James Lowe, Mack Hansen and Keith Earls sealed a comprehensive victory.
Replacement prop Kyle Sinckler crossed for England, but it was scant consolation on a difficult evening when stuttering World Cup preparations were thrown into further disarray.
"Whilst I'm incredibly disappointed with the result, the players kept fighting," said Borthwick.
"I thought the players that came off the bench added on the pitch.
"Just before half-time at 7-3, we missed some opportunities and turned over ball in the final third, so we weren't able to put enough pressure on them.
"When it was 15 against 15 it was a tight battle, unfortunately it didn't stay 15 on 15."
Ireland retained their place at the top of the world rankings courtesy of a 12th successive win.
Earls stepped off the bench to mark his 100th cap in style with his 36th international try as the hosts overcame a disjointed opening period.
Head coach Andy Farrell said: "It had a bit of everything: good, bad and ugly.
"I wasn't too happy at half-time. We had them in a place where we could push a little bit harder and make it a little bit easier for ourselves but we didn't kick on.
"I was really pleased that we found or rhythm back into the game. I thought we scored some great tries."
