The tourists, electing to bat in overcast conditions, slumped to 56-3 before Khan's rescue act helped them recover to 261-4 when bad light ended play two overs early at the Galle International Stadium.
The 36-year-old middle-order batsman, who came to bat in his 90th Test at 19-2, hit 11 boundaries and a six in his 24th century. Only Inzamam-ul Haq (25) has more Test hundreds for Pakistan.
Skipper Misbah-ul Haq, making a typically dour but determined 31, put on 100 for the fourth wicket with Khan before he was caught behind off left-arm spinner Rangana Herath.
Asad Shafiq ensured the effort did not go waste as he saw off the second new ball to help Khan add 105 for the fifth wicket, himself returning unbeaten at close on 55.
Pakistan's coach Waqar Younis said he was delighted at the total his team was able to post after the early setbacks.
"Any coach or captain will be proud of that," the former fast bowler said. "It all boiled down to experience. Younis has tons of it and so does Misbah.
"There was a lot of talk at home of whether Asad Shafiq deserved to be in the side. He showed today that he belongs to the highest level."
Waqar said it was a bold decision by the team management and the captain to bat first despite favourable overcast conditions for the bowlers.
"With so much rain around, there is bound to be some juice in the wicket and I thought we were very bold to bat first. That paid off because the wicket eased up by afternoon."
Sri Lanka's coach Marvan Atapattu admitted it was hard work for the bowlers after the morning session.
"The moisture dried up and it became easy to bat out there," he said. "I think we have done well to keep them down to 261, but a lot still remains to be done.
"This is a wicket that usually plays well on the first two days, but spin is going to be a factor later in the match."
Khan was given a reprieve by the Decision Review System (DRS) when he was on 59 after umpire Bruce Oxenford had declared him leg-before to off-spinner Dilruwan Perera.
Television replays showed the ball pass over the stumps.
The partnership between Khan and 40-year-old Misbah came after Sri Lanka dominated the morning session with three quick wickets.
The start was delayed by 30 minutes due to a wet outfield caused by overnight rain. Bad weather has been forecast on all five days of the Test.
Both teams went in with two spinners -- Saeed Ajmal and Abdur Rehman for Pakistan, and Herath and Perera for the hosts -- hoping the grassless pitch provides some turn later in the match.
Former Sri Lankan captain Mahela Jayawardene, who is retiring from the longer format after the two-Test series, walked out to field amid bursting firecrackers as school children gave him a guard of honour with raised bats.
Giant posters of the elegant batsman, who is sixth in the all-time scorers' list with 11,671 runs in 147 Tests, adorned the Galle International Stadium where some 2,000 home fans were present.
Sri Lanka: Angelo Mathews (capt), Kaushal Silva, Upul Tharanga, Kumar Sangakkara, Mahela Jayawardene, Kithuruwan Vithanage, Niroshan Dickwella, Rangana Herath, Dilruwan Perera, Shaminda Eranga, Dhammika Prasad.
Pakistan: Misbahul Haq (capt), Ahmed Shehzad, Khurram Manzoor, Azhar Ali, Younis Khan, Asad Shafiq, Sarfraz Ahmed, Saeed Ajmal, Abdur Rehman, Mohammad Talha, Junaid Khan.
Umpires: Ian Gould (ENG) and Bruce Oxenford (AUS)
TV umpire: Richard Illingworth (ENG)
Match referee: Andy Pycroft (ZIM)
COMMENTS (2)
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Younus khan has earned my respect.He is a great player.And he was fully fit to do this job.From a player of his caliber and determination i very much expected this.His way of dealing with the spin attack and negotiating with the fast bowlers is a world apart from the method that the members of his team apply.Others should learn from his technique.
Thank you, Younus.And please continue with the great work.Pakistan needs you.
Bad move to include Khurram Manzoor in the team. Shan Masood has a way better technique and is the future of Pakistan test cricket. Manzoor has a shaky technique and will not last outside of Dubai and Sharjah. Shan Masood should replace Manzoor for next test.