Nemati, 30, secured both Olympic and Paralympic qualification quota places for her nation last year.
The Iranian Olympic Committee agreed to the decision after a suggestion from the country's National Paralympic Committee.
Nemati will carry the Iranian flag at the ceremony which takes place at the Maracana on 5 August.
"I will do my best to win honours in Olympic and Paralympic Games simultaneously and I dedicate a gold medal to my family," she said.
Nemati won Paralympic gold in the women's individual recurve W1/W2 at London 2012, becoming the first Iranian woman to win an Olympic or Paralympic title.
She earned the Olympic qualification slot with a superb performance at the 2015 Asian Archery Championships in Bangkok, Thailand where she won silver in the women's recurve.
The Iranian Paralympic Committee said it hoped the suggestion to its Olympic counterparts would send a message from Paralympians to Olympians and also to the world, that a person's disability is not a limitation.
The last archer to compete in both Games in the same year was Italy's Paola Fantato at Atlanta 1996.
Paralympic archer Zahra Nemati has been chosen to be Iran's flagbearer at the Rio 2016 Olympics.