The women's selection committee was forced to make this change after pace spearhead Goswami suffered an injury to her heel ahead of the first T20 International.
The pacer recently became the first female cricketer to take 200 ODI wickets in the second match against South Africa, which India won by 178 runs at Kimberley.
Goswami, an ICC Women Cricketer of the Year in 2007, had earlier broken Australian Cathryn Fitzpatrick's record of highest wickets in women ODIs.
India Women's T20I squad:
Harmanpreet Kaur (captain), Smriti Mandhana (vice-captain), Mithali Raj, Veda Krishnamurthy, Jemimah Rodrigues, Deepti Sharma, Anuja Patil, Taniya Bhatia (wicket-keeper), Nuzhat Parveen (wicket-keeper), Poonam Yadav, Rajeshwari Gayakwad, Shikha Pandey, Pooja Vastrakar, Radha Yadav, Rumeli Dhar.