Younis hit 200 not out to enable Pakistan to declare on 419 for nine, setting Zimbabwe an unlikely 342 to win.
Zimbabwe were 13 for one at the close, losing opening batsman Tina Mawoyo in the last over of the day, leg before wicket to Saeed Ajmal.
Off-spinner Ajmal, who took seven for 95 in the first innings, will be the main threat to the Zimbabwe batsmen on the last day on a deteriorating pitch.
Pakistan were in deep trouble at 23 for three early in his innings. He shared a century partnership with captain Misbah-ul-Haq on Thursday but the tourists were still vulnerable when Asad Shafiq was bowled in the first over on Friday, with Pakistan only 91 ahead with five wickets remaining.
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Another century stand, with wicketkeeper Adnan Akmal, who made a career-best 64, steered Pakistan towards safety. An unbroken last wicket partnership of 88 with Rahat Ali (35 not out) took the game away from a tiring Zimbabwe team.
Misbah delayed the declaration, first signalling two more overs as Younis neared a double century, then indicating a further over when Younis was on 194 when the allotted two were complete. Younis hit off- spinner Prosper Utseya to reach the landmark and the declaration was immediate.