Farrell was shown a yellow card, upgraded to red, after his shoulder hit Taine Basham with the sort of no arms tackle that he has made something of a trademark.
He faces an almost certain three-game ban, meaning he would miss England's final two warm-ups v Ireland and Fiji and their World Cup opener against Argentina.
"Regarding Owen, we'll wait and see what happens," Borthwick said after a game littered with cards. "The same with Jack van Poortvliet (who went off injured). He'll get a scan. Rather than jump to any conclusions, we'll wait and see what happens."
England were largely toothless for an hour but came to life when reduced to 12 men, clawing their way to victory with a Maro Itoje try and a George Ford penalty.
"As this builds, I want to make sure we've got fundamentals in place," Borthwick said. "Our set piece, our kicking game and defence were in a strong position. The attack is the final building block and takes the longest to come, but that's what we're working on.
"We wanted to name the 33 (for the World Cup) this week so we had clarity, I know we'll need to adapt over the next couple of months."
Wales coach Warren Gatland was fuming after his 15 men somehow allowed England back into the game. "I am furious actually, I am hugely disappointed but we found out about a few people today.
"It is just about some game management when we had them on the ropes and we just let them off the hook which is disappointing and answered a few questions. We gave away from soft penalties at key moments, with the yellow card as well.
"The biggest question of them answered is players knowing their roles in certain positions which was disappointing.
"We will see next week about selection but we need to be much better than we were today for next weekend (against South Africa). That was a game we should have won and we cost it ourselves."