Hamid Ansari was convicted on charges of spying after he was found with a fake Pakistani identity card.
But his supporters said he had entered the country to pursue “blind and stupid” love with a woman he met online.
It is not clear, however, if he ever met the woman he crossed the border for. Ansari was greeted at India’s Wagah border by his family, government officials and journalists.
His return ends a years-long ordeal for his family who fought to first track him down, and then secure his release. Though officially convicted in 2015, Ansari had been in Pakistani custody since 2012.
His jail term officially ended on Sunday, but his release was delayed because legal formalities had not been completed.
India and Pakistan have fought three wars since independence and the partition of India in 1947 and regularly jail each others citizens.
Hamid Ansari is the youngest son of Fauzia Ansari, the vice-principal of a Mumbai college, and banker Nihal Ansari.
In November 2012, the 33-year-old had just started a new job as a lecturer at an educational institute when he told his parents that he was going to Afghanistan for an interview with an airline company.
But a few days after he landed in the Afghan capital Kabul, Ansari went missing. His family says that he stopped communicating with them, and his phone number was switched off.
Activist Jatin Desai, who has been at the forefront of efforts to get Ansari released, told BBC Hindi that that the family had then checked his laptop, where they discovered that he had been communicating with several people from Pakistan via email and social media.
After his family was unable to trace his whereabouts in Pakistan, they reached out to government officials and activists for help.
Among them was Mr Desai, who has been working for many years to secure the release of both Indian and Pakistani prisoners jailed in each others countries.They had also realised that he was in the Khyber Pakhtunkhwa province of the country.
A Pakistani journalist – who was later detained for a long period – managed to get in touch with Hamid’s mother in Mumbai and filed a missing person’s petition in court on her behalf.
She played an important role in encouraging a government commission on enforced disappearances to investigate his case.
As a result, security agencies, in early 2016, eventually admitted that Ansari was in their custody and had been jailed.