The 23-year-old Commonwealth Games silver medallist finished on the podium after she shot 205.9 in the eight-woman final, same as gold medallist Najmeh Khedmati of Iran, but lost out on the top prize as she managed 9.9 to the Iranian's 10.1 in the shoot-off here.
Pooja recorded 184.5 after leading the field till the 17th shot. An 8.8 in the 18th attempt proved to be her undoing on day three of competition in the continent's last quota event for Rio Games at the Dr. Karni Singh Shooting Range.
The competition inside the 10m air rifle range was intense as the participants produced some excellent shooting, with scores rarely going below 10.
In the men's 50m pistol, Omkar Singh could not make the podium as he finished fifth after shooting 147.0 in the final.
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Thanks to Ayonika's effort, India have equalled the number of quotas it secured ahead of the 2012 London Olympics.
In the women's 10m air rifle event there were two quota places available. However, India were eligible for only one (each country can win a maximum of two quotas per event) as Apurvi Chandela had already secured one quota in the event in earlier competitions.
Pooja and Ayonika were in gold and silver positions till the 18th shot when the former shot 8.8 to be relegated to bronze medal position.
Khedmati, who is a world number 10 and already had a quota secured in the event, was steadily catching up with the Indians and finally caught up with Ayonika in the 20th shot and both tied at 205.9 to go into a shoot-off for gold and silver. The quota secured, Ayonika shot a disappointing 9.9 in the shoot-off to Khidmati's 10.1.
Elated at having secured a quota Ayonika said, "The last two shots are still ringing in my mind. I was here to win the gold but the Iranian finished strongly. I will start training again from tomorrow morning itself to ensure I improve on my first and last shots. I am happy at having won the quota but disappointed at losing out on the gold."
In the day's other event, men's pistol Japan's former world champion and world number 6 Tomoyuki Matsuda won the gold beating two North Koreans Song Guk Kim who claimed silver and Jong Su Kim who won the bronze.
Omkar finished fourth in an event, where India had already exhausted its quotas through Jitu Rai and Prakash Nanjappa.
With four days more to go in the event, the Indian shooting squad looks set to go one better than London as far as quotas are concerned.