Shiffrin, the most successful Alpine skier in World Cup history with a record 108 victories, arrived in Cortina in strong technical form after winning seven of the eight slaloms this season, and Johnson's downhill run put the USA at the top of the standings.
"I didn’t quite nail it. I didn’t quite find a comfort level that allows me to produce full speed," she told reporters.
"I want to be careful not to make excuses, because it's not really an excuse. It's just that the work we've done, I've been so prepared for so much, for all the slaloms this year. So there's something to learn from this day, and I'm gonna learn it."
Four years after drawing an unexpected blank that left her doing a lot of soul-searching at the Beijing Olympics, the 30-year-old stressed the result was not about confidence but the subtle sensations that define elite Alpine ski racing, describing the sport as one of "fine margins and a lot of variables," particularly in conditions the skiers had not encountered this season.
On soft, spring-like snow, Shiffrin never found her groove on the Olimpia delle Tofane.
"I guess it's, like, sometimes I'm really nervous, sometimes I'm settled, sometimes I don't even know what's a race day. So it's entirely different, and I don't even know how to explain it," she said.
Shiffrin had drawn inspiration from Johnson’s downhill performance - coming only two days after her teammate’s gold-medal triumph in the individual event - and said racing for a partner can sharpen motivation even if the mindset differs slightly.
Shiffrin now has five days until the giant slalom to find out what went wrong.
"I think we always do better with more information, and I got a lot of information today," she said.
Despite missing out on what would have been her first Olympic medal since the 2018 PyeongChang Games, she pointed to a broader positive for the USA team, with Paula Moltzan and Jacqueline Wiles securing bronze.
"We become champions from negative experiences in many ways," said Shiffrin, whose best result in Beijing was fourth in a team event.