The pair surpassed Bangladesh's previous highest fifth-wicket stand of 144, set by Mehrab Hossain jnr and Mushfiqur Rahim against New Zealand in 2008, to steer the team away from early trouble after a strong opening spell from Pakistan's Aizaz Cheemer
The stand was also Bangladesh's highest against Pakistan besting the 167 of Javed Omar and Habibul Bashar in 2003.
Shakib was unbeaten on 108, for his second test century while Nafees fell to an awkward bouncer off Umar Gul on 97.
Wicketkeeper Adnan Akmal took a simple catch after the ball hit Nafees on the glove, ending his solid 177-ball innings that featured 12 boundaries.
Seamer Cheema had taken advantage of the bowler friendly conditions to claim three wickets and help reduce Bangladesh to 43-4 after play had been delayed by more than an hour because of dense fog
The 32-year-old medium-pacer claimed had opener Nazimuddin (0) out leg before wicket with only his sixth delivery.
Gul then removed the under-performing Tamim Iqbal (14) when the Bangladesh opener's attempted hook shot was caught by Cheema at backward fine leg.
Cheema returned to bowl out Mahmudullah for a first-ball duck to leave the home side, who need to win the match to level the series after an innings defeat in the first test, struggling on 21-3.
Nasir Hossain (7) was next to go in the 14th over when he edged a simple catch to wicketkeeper Adnan Akmal off the bowling of Cheema.
Bangladesh: Tamim Iqbal, Nazimuddin, Shahriar Nafees, Nasir Hossain, Shakib Al Hasan, Mushfiqur Rahim (capt & wk), Mahmudullah, Elias Sunny, Shahadat Hossain, Robiul Islam, Nazmul Hossain
Pakistan: Mohammad Hafeez, Taufeeq Umar, Azhar Ali, Younis Khan, Misbah-ul-Haq (capt), Asad Shafiq, Adnan Akmal (wk), Abdur Rehman, Umar Gul, Saeed Ajmal, Aizaz Cheema
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