Khan inaugurated the corridor by removing a curtain that was lifted by hot air balloons. A huge 'kirpan' (dagger) was displayed at the inauguration site.
"I was not aware of the importance of the Kartarpur till a year ago," Khan told a gathering of over 12,000 devotees, including former prime minister Manmohan Singh and cricketer-turned-politician Navjot Singh Sidhu.
Guru Nanak Dev spent last 18 years of his life at Kartarpur Sahib.
Khan welcomed the first batch of the Indian Sikh pilgrims who entered Pakistan through the corridor which links Gurdwara Darbar Sahib in Pakistan, the final resting place of Guru Nanak Dev, to Dera Baba Nanak shrine in Punjab's Gurdaspur.
Earlier, Foreign Minister Shah Mehmood Qureshi said the doors of Kartarpur have been opened for Sikh pilgrims.
"If the Berlin Wall can be demolished, if the Kartarpur Corridor can be opened, then the temporary boundary of the Line of Control can also be ended," Qureshi said, invoking the Kashmir issue during his address on the occasion.
Prime Minister Narendra Modi earlier flagged off the first batch of over 500 pilgrims in Gurdaspur, saying it will be easy to pay obeisance at the Darbar Sahib gurdwara after the opening of the Kartarpur corridor.
Asserting that he is fortunate to be able to dedicate the Kartarpur corridor to the country, Modi said the opening of the corridor and the integrated check post will bring double happiness to the people.
The first 'jatha' also include Akal Takht Jathedar Harpreet Singh, Punjab Chief Minister Amarinder Singh, former chief minister Parkash Singh Badal, Sukhbir Singh Badal and Harsimrat Kaur Badal.
The Shiromani Gurdwara Parbandhak Committee members and all the 117 MLAs and MPs from Punjab including ministers are also part of the first 'jatha'.
Prime Minister Khan, who congratulated the Sikh community on the 550th birth anniversary of Guru Nanak Dev, said the historic opening of the Kartarpur corridor is a testimony to Pakistan's commitment to regional peace.
"We believe that the road to prosperity of region and bright future of our coming generation lies in peace," Khan said in his message on the occasion.
"Today we are not only opening the border, but also our hearts for the Sikh community," he said.
Khan said the unprecedented gesture of goodwill from his government was a reflection of its deep respect for Guru Nanak Dev and religious sentiments of the Sikh community.
Pakistan believes that interfaith harmony and peaceful coexistence would provide an opportunity to work for larger interests of the people of the sub-continent, he said.
Notwithstanding their strained ties, India and Pakistan signed an agreement last month, paving the way for the inauguration of the Kartarpur corridor. According to the pact, Pakistan will allow 5,000 Indian pilgrims daily to visit Gurdwara Kartarpur Sahib.