The inauguration comes ahead of the 550th birth anniversary of Guru Nanak Dev, the founder of Sikhism, on November 12.
"Want to congratulate those worked on the temple," Geo News quoted Khan as saying while ddressing the inauguration ceremony here.
"I did not know my government was so efficient. Want to congratulate them again for completing the complex in record time."
Khan arrived at the corridor inauguration ceremony using the shuttle service being used by pilgrims. He was accompanied by Foreign Minister Shah Mehmood Qureshi, Special Assistant on Information Firdous Ashiq Awan, Senator Javed Khan, Special Assistant to the Prime Minister for Overseas Pakistanis Zulfi Bukhari and other officials.
The shrine is where Guru Nanak Dev spent 18 years of his life and is his final resting place.
Meanwhile, former Indian Prime Minister Manmohan Singh led the first delegation of Sikh pilgrims as they crossed into Pakistan through the Kartarpur Corridor. Punjab Chief Minister Amarinder Singh was also part of the 'jatha' (caravan).
"I hope India and Pakistan relations improve enormously as a result of this beginning," Manmohan Singh told PTV as he walked towards the Pakistan side, terming the occasion a "big moment".
Amarinder Singh told Dawn news they were all happy because it had been a desire of Sikhs to visit their religious sites in Pakistan for 70 years.
"This is a beginning, I hope it's going to continue and many more gurdwaras are going to be allowed," he added.
Former Indian cricketer-turned-politician Navjot Singh Sidhu was also in attendance at the inauguration ceremony and thanked Khan for taking the bold step to build the Kartarpur Corridor "without looking at gains or losses".
Before seeing off the first group of pilgrims from India, Prime Minister Narendra Modi addressed members of the Sikh community and hailed the opening of the corridor.
"I also thank Pakistan's Prime Minister Imran Khan for understanding India's wishes and turning Kartarpur into reality," Modi said in his speech.
Meanwhile, members of the Sikh community on Saturday continued to arrive from all over the world, according to Geo News.
About 8,000-10,000 pilgrims are expected to arrive from around the world to mark Guru Nanak's 550th birth anniversary.
To facilitate the Sikh yatris, the Pakistan government has installed 130 counters, where their passports will be confirmed or scanned, and permit will be verified.
( With inputs from IANS )