The 45-year-old athlete won the silver medal with her throw of 4.61 meters in her six attempts.
With this win, India has won third medal in the ongoing Paralympics. Malik now will receive a cash award of Rs 4 crore under Haryana Sports Scheme for winning the silver medal.
Bahrain's Fatema Nedham clinched the gold medal with the best throw of 4.76m while Greece's Dimitra Korokida bagged the bronze medal with a throw of 4.28m.
Malik is a paraplegic, paralysed from waist down and mother of two and wife of an Army officer. (President, PM and others congratulate golden boy Mariyappan Thangavelu)
After bagging the silver, an excited Deepa said she wants to use the medal to support women with disabilities in India.
The 45-year-old, who is the oldest in the Indian contingent in Rio to win a medal, called it a "proud moment" for her and the family.
"I want to use this medal to support women with disabilities in India. This journey has been wonderful for me and my entire family, I am proud to be the oldest athlete in the team and win a medal," Deepa told IANS immediately after her feat.
Deepa has thus confirmed India's third medal from the Paralympic Games. India's tally at this edition of the Paralympics now stands at one gold, one silver and a bronze.
Mariyappan Thangavelu had won gold in the Men's High Jump T42 category on Friday with fellow Indian Varun Bhati taking bronze in the same event.
Deepa also became the first Indian female medallist in the history of the Paralympic Games. India, who made their Paralympic Games debut in 1968, have bagged an overall total of 11 medals including three gold, four silver and an equal number of bronze medals.
Deepa who received the prestigious Arjuna award in 2012. She is the mother of two children and the wife of an Army officer.
She has registered her name twice in the Limca Book of Records, once for crossing a 1 km stretch of the Yamuna river against the current in 2008, and then again for covering 58 km by riding a special bike in 2013.