The 19-year-old Fernando, who is a left-arm fast-medium bowler, has been called up after performing well for Sri Lanka under 19 sides.
Karunaratne, a regular test opener, was left out of the first test against Pakistan at Galle in favour of fellow left-handed opener Upul Tharanga.
The pair replace injured seamers Nuwan Pradeep and Suranga Lakmal. Fast bowler Shaminda Eranga has been named in the squad subject to proving his fitness.
"Eranga has a tightening of his upper quad muscles and is being monitored carefully," Sri Lanka manager Michael de Zoysa said.
"He didn't bowl at full pace during the Pakistan second innings and complained of stiffness the day after the match."
Sri Lanka won the first test by seven wickets to go one-up in the two-test series.
The second test marks the final appearance of former captain Mahela Jayawardene who will retire from the longer format of the sport to concentrate on one-day internationals.
Sri Lanka test squad: Angelo Mathews (captain), Upul Tharanga, Kaushal Silva, Kumar Sangakkara, Mahela Jayawardene, Kithuruwan Vithanage, Niroshan Dickwella, Rangana Herath, Dilruwan Perera, Shaminda Eranga, Dhammika Prasad, Lahiru Thirimanne, Chanaka Welegedara, Dimuth Karunaratne, Binura Fernando.
(Editing by Michael Hann)
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