The time by Atkins is the second fastest in the world this year, trailing only Sanya Richards (49.86).
Atkins became the second Auburn woman to win the NCAA 400, joining Olympian Juliet Campbell, who took the title in 1993.
With the victory by the sophomore, Auburn has produced an individual NCAA champion for 11 straight years.
For the men, whose top finish was second in the high jump by freshman Ryan Fleck on Friday night with a jump of 7-3 1/2, it was a 12th place team finish as the Tigers scored 18 points. The women's team finished 25th with 11 points as Texas A&M claimed both the men's and women's titles. The Auburn women scored 11 points to finish 25th.
"I was a little nervous so I told myself to just run, and I did and I'm so thankful," Atkins said after her victory. "I decided if they wanted to beat me they had to come get me. I knew I had a 50 (seconds) in me and it was a little discouraging because I have been a little inconsistent, but I'm just very excited that that 50 finally came."
Atkins, who is also outstanding in the shorter sprints, only competed in the 400 in the individual events as the Auburn coaches decided that would give her the best chance to make a splash and she did.
For the men on the fourth and final day of competition on the campus of the University of Arkansas, a freshman was the top performer as Marcus Rowland finished third in the 200 meters. Running into a headwind of 1.6 miles per hour, he ran a 20.82 to take behind Charles Clark of FSU (20.55) and Rondell Sorillo of Kentucky (20.70).
"I'm usually hard on myself, but coming out of lane one and getting third I'm pretty happy with my performance," Rowland said. "I think it was my warm-up. My coaches were there and helped build up my confidence, and that's always good. It helped motivate me."
In the women's 200 on Saturday, sophomore Cache Armbrister ran a time of 23.80 to finish seventh.
"We had some young kids that really stepped up these last two days," Auburn head coach Ralph Spry said. "I knew coming in we had a young team and we were hoping to crack the Top 10 in both races, but we ended this meet on a high note. We return all but two people next year so we're setting the stage for the next couple of years, which should be pretty exciting. I'm proud of how we lined up this weekend and finished what we started."
In the men's competition Texas A&M scored 48 points to edge Florida, FSU and Oregon, which tied for second with 46 points. In the women's events, Texas A&M scored 50 and was followed by Oregon with 43 and Arizona State with 41.
Eight Tigers earned All-American honors in the four days of competition. The group includes:
Sophomore Cache Armbrister (women's 200)
Sophomore Joanna Atkins (women's 400)
Sophomore Michael DeHaven (men's 4x100m relay)
Freshman Ryan Fleck (men's high jump)
Sophomore Stephen Fly (men's 4x100m relay)
Freshman Girma Mecheso (men's 10,000)
Freshman Marcus Rowland (men's 200, 4x100 relay
Senior Jerod Wims (men's 4x100m relay)