Competing in the fifth and final heat of the event, Merrill finished ninth with a time of 57.15, which was a season best but not enough to qualify for the semifinals.
A former NCAA Champion for the Tritons, Merrill was competing for Sri Lanka and was one of just two athletes to represent the island nation at the 2012 Olympic Games.
"Today was (a) moment I will never, ever forget," Merrill posted on her Facebook page after the race. "The roar of the crowd (was) so loud it made my heart echo. The bounce of the rock-hard track. The feeling of the Olympic Spirit. Thank you Sri Lanka and thank you to you all for sharing it with me!"
Great Britain's Perri Shakes-Drayton won the heat at 54.62, followed by Melaine Walker of Jamaica at 54.78, Ukraine's Hanna Yaroshchuk at 54.81 and Morocco's Hayat Lambarki at 55.58.
The top four individuals from each heat and the next four fastest overall qualified for the semifinals, which will begin Monday evening. The final is scheduled for Wednesday.
Merrill owns the Sri Lankan national record in the 400 hurdles after clocking a time of 56.83 at the Asian Athletic Championships in Japan last summer. She was selected as the country's female Olympic wild card entrant in early July after no Sri Lankan athlete was able to reach a qualifying standard.
Click here for complete results from the women's 400-meter hurdles. For more on Merrill's big day, read Mark Zeigler's story in the U-T San Diego here.