Smriti, who represented Southern Brave, will fly back home to spend time with her family before embarking on the tour of Australia in September. She will be replaced by Ireland's Gaby Lewis. She will miss the last two matches for the Brave, including the final.
"I would love to be able to stay with the team until the final, but we've been away from home for a long time with more tours ahead. I'll be watching the team at Lord's and hoping they can continue our good form. It's been a fantastic competition to be involved in and I've really enjoyed it.," said Smriti in a statement.
Harmanpreet, who was playing for Manchester Originals, has a quadriceps injury. A replacement will not be sought by her team, who are at the bottom of the table.
Smriti's final innings for Southern Brave came on Wednesday when she hit 78 runs off 52 balls to lead her side to victory over Welsh Fire. For her scintillating knock, she was adjudged as the 'Player of the Match'.
In total, Smriti scored 167 runs in seven innings at a strike rate of 133.60. Harmanpreet, on the other hand, amassed 104 runs from three innings at a strike rate of 109.47.
This leaves Shafali Verma playing for Birmingham Phoenix, Deepti Sharma representing London Spirit and the top run-scorer of the tournament, Jemimah Rodrigues for Northern Superchargers as the remaining Indians in The Hundred.