The Auburn senior got a slow start off the block and finished third in 21.65 seconds. Vanderpool-Wallace's time in the prelims, 21.46, was the fastest of the day as Liv Jensen of Cal won the finals in 21.48.
Auburn is in fifth place with two days of competition remaining. Cal leads with 132 points while Southern Cal and Stanford both have 188 points. Arizona is fourth with 107, Auburn has 94 points and Georgia is sixth with 91.
"We are ahead of where we want to be," Auburn coach Brett Hawke said of his team's score.
"At a meet like this, you always get some points you don't expect, and you always lose some you don't expect. It's just the way it is. I'm pretty happy with where we are right now, in fifth place. We know it's a long meet. There are six sessions; that's just two. We've got a long way to go, and we're going to come back tomorrow and fight in the morning."
Another Auburn senior, Vennie Dantin, took third place on Thursday night. Dantin's finish came in the one-meter springboard diving event.
AU diving coach Jeff Shaffer liked what he saw out of Dantin. "It was a great performance," he said. "She did an outstanding list in the prelims to put herself in a position to dive in one of the most competitive finals I've witnessed. It came down to the fifth and sixth round with anybody really having a chance to win.
"I'm so proud of the way she stepped up and competed," the coach added. "It was a personal-best for her on one-meter, and that's the way you want to go out as a senior."
Tory Ishimatsu of Southern Cal won with a score of 354.10. Jasie Patrick of Texas A&M was second with 348.9 points while Dantin finished with 337.60. Dantin's score was a personal-best in the event and her best NCAA finish.
The first points of the event for the Tigers came in the opening race as the team of Vanderpool-Wallace, junior Hannah Riordan, sophomore Haley Krakoski and sophomore Emily Bos finished fifth in the 200-yard freestyle relay. Auburn's time in the event was 1:27.86. Cal finished first with a time of 1:27.11.
The Tigers also took fifth place in the final event of the evening, the 400 medley relay. Auburn's time was 3:30.38 with Bos, junior Lauren Norberg, sophomore Olivia Scott and Vanderpool-Wallace swimming. Cal won with a time of 3:28.10, an NCAA record.
Hawke said he deserved the blame for Vanderpool-Wallace not repeating as champion in the 50.
"In the quest to try and shave hundredths of seconds off and swim phenomenal times, you try different things," Hawke said of the senior's third-place finish. "Sometimes they work, sometimes they don't. She's giving it 100 percent out there. I feel like in a way I messed her up a little bit. She's always giving her best effort."
Vanderpool-Wallace said, "I'm going to come back in the 100 and swim as fast as I can. I'm disappointed, more in myself than losing the race. I went into the race knowing it was my start that I needed to work on, and I still didn't do what I needed to do so I'm definitely motivated for the 100 freestyle. That race is my baby. I'm not going to lose that."
Cal's Jensen, who has struggled to beat Vanderpool-Wallace, was excited about the victory on Thursday night. "Honestly, I have been thinking about it for a long time," she said.
"The way I think about it is, people say she's (Vanderpool-Wallace) the defending champion, but no one had won this race yet. I knew I could do it and I knew I had the motivation. She is a great racer and it was a great race."
The championships will run through Saturday. Prelims begin at 11 a.m. each day and the finals start at 7 p.m.