Wilson, 22, is a model and beauty pageant titleholder who was crowned Miss Universe Australia earlier this year.
Miss Nicaragua, Sheynnis Palacios, was the first from her country to wear the coveted crown.
She is 23-year-old communicologist, who said she wants to work to promote mental health after suffering debilitating bouts of anxiety herself.
Miss Thailand, Anntonia Porsild, was first runner-up.
Australia's Moraya Wilson is second runner-up in the 72nd Miss Universe competition.
Eighty-four women competed for the crown in the 72nd edition of the competition.
Palacios appeared to secure the win late on Saturday night when she confidently answered the question of which woman's shoes would she like to spend a year in by saying Mary Wollstonecraft, the 18th-century English writer and philosopher. Wollstonecraft was an advocate of women's rights and is considered one of the forerunners of feminism.
Palacios said she wants to work to close the salary gap between the genders so that women can work in any area.
Miss Universe was last held in El Salvador in 1975. This year's event was another opportunity for President Nayib Bukele to tout changes made under his administration, especially greatly improving the country's safety.
"El Salvador has changed for good and we have shown it again," Bukele said Saturday night.
"Miss Universe has given us the opportunity to show the world what we are capable of. Thank you for choosing to be part of El Salvador's rebirth."
Bukele is running for re-election despite constitutional term limits and is widely popular for his crackdown on the country's gangs. But he has faced international criticism for eroding checks and balances on his power and not respecting human rights.
More than 72,000 people have been arrested without due process since a state of emergency was declared in March 2022 in response to a surge in gang violence. The special powers it granted Bukele remain in place.
8°C