She won a silver with an impressive throw of 4.61m (15.12ft) in the F-53 final event on Monday in Rio.
Her medal has taken India's tally to three after high jumpers Mariyappan Thangavelu and Varun Bhati won gold and bronze respectively on Saturday.
Many in India have taken to Twitter to praise her historic achievement.
Malik's win also means that India's Paralympians have already outperformed India's Olympic contingent of more than 100 athletes.
India won two medals - silver and bronze - at the Rio Olympics.
Malik said she felt "incredible to fulfil a lifelong ambition".
"This is our third medal now in Rio and I sincerely hope people back home wake up and acknowledge the potential of para sports in India," she added.
And many Indians, including Prime Minister Narendra Modi and Bollywood star Amitabh Bachchan, woke up to the news and praised Malik's performance.
Malik was paralysed below her waist in 1999 after undergoing  surgery to remove a spinal tumour.
She decided to participate in para sports six years later and took to swimming and javelin throw, winning medals at national and international events.
But she also participated in the shot put, winning silver at the World Championships in 2011.
On Monday, she thanked her coaches and everybody who supported her.
"It is an extremely satisfying feeling and a big thank you to everyone who has supported me over the years," she said.
Shot-putter Deepa Malik has created sporting history after becoming the first Indian woman to win a Paralympics medal.