Indian diplomat Surjeet Sindh, who was declared persona non grate on Thursday night, has formally left for India along with his family on Saturday.
The Foreign Secretary had summoned the Indian High Commissioner and conveyed the decision of the government of Pakistan to declare Surjeet Singh, an official of the Indian High Commission, as persona non grata.
The Foreign Secretary had expressed deep concern over the activities of the Indian official that were in violation of the Vienna Convention and the established diplomatic norms.
Tensions between India and Pakistan have soared since a militant attack last month on an Indian army base near the de-facto border dividing Kashmir killed 19 Indian soldiers.
India blamed militants in Pakistan and said it had responded by carrying out strikes across the heavily-militarised border, although Islamabad denies these took place.
Tensions were already high before the attack, with deadly violence in Kashmir over the death on July 8 of a popular freedom fighter Burhan Wani.
More than 100 people, most of them young protesters, have been killed in clashes with security forces in Indian-Occupied Kashmir.
Kashmir has been divided between India and Pakistan since their independence from Britain in 1947. Both claim the territory in full and have fought two wars over the mountainous region.