Thar Express, the train which plies every week between Jodhpur and Karachi, reached Munabao railway station on Saturday evening with 62 Indian and 103 Pakistani passengers on board.
The train had departed from Zero Point station in Pakistan at 5:20 pm and reached Munabao station on the Indian side at 5:40 pm today.
Pakistan on Friday announced to stop the weekly train after the Central government stripped Jammu and Kashmir of its special status by scrapping Article 370 of the Constitution.
Pakistan has also suspended the operation of Samjhauta Express, which runs between Delhi and Attari in India and Lahore in Pakistan.
The decision to suspend the two trains is in line with Islamabad's other moves to remonstrate against Indian move, including suspending bilateral trade and downgrading of diplomatic relations.
Indian Railways on Thursday had clarified that the Samjhauta Express has not yet been suspended but Pakistan authorities refused to send their crew to India citing security concern.
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The train stood on the Wagah side of the border in Pakistan with around 110 passengers yesterday. An Indian engine brought the train from Wagah to Attari.
Calling its steps in Jammu and Kashmir an "entirely internal affair", India has rejected Pakistan's unilateral move to downgrade diplomatic ties and asked Islamabad to review its decision so that normal channels for diplomatic communications are preserved.