Heavy rains forced the evacuation of nearly 200,000 people from their homes, police said on Saturday.
The Indore-Gandhinagar Shanti Express and its passengers were submerged on Thursday morning by flood waters raging through parts of India, after a lengthy heat wave.
"All the passengers have been saved by army soldiers and local police," said Director-General of Police A K Bhargava, the police chief of Gujarat state. "All of them have been moved to safer places."
The rescue was carried out late on Friday and there were no casualties, he said.