Punia had reached Patiala from Minsk, where she had taken part in Belarus Open Championship last week, in the wee hours on Sunday.
She went past the 60m mark on four of her five legal throws and found the power to breach the Olympic qualifying mark in her fourth try.
She will be taking part in her fourth Olympics after the 2004, 2012 and 2016 editions of the Games.
Without a world ranking since she was nursing a glutes (muscles of buttocks) injury, Punia was taking part in only her third competition since the 2018 Asian Games.
She threw 62.64m in the Federation Cup here in March and after managing 58.62 in Minsk on June 25, she secured her ticket to Tokyo Games with her first throws of over 63m since August 2004 in Kiev.
"I know I can throw farther with my training but I was wary of aggravating the issue with my glutes muscles. I have worked hard over the last two and half years since the Asian Games and am happy that I could secure qualification today," Punia said.
"I will consult the Athletics Federation of India and draw up my training programme for the Olympic Games," she added.
Punia will be the second Indian woman to take part in the event in the Tokyo Olympics after national record holder Kamalpreet Kaur, who threw the iron disc to a distance of 66.59m in the Indian Grand Prix 4 on Monday last.
Kaur did not start in the event on Tuesday, though her name was there initially.