At the Harare Sports Club, Pakistan were 87 for three at tea, a slender lead of nine runs.
Younis and Misbah came together after Pakistan, trailing by 78 runs on the first innings, slipped to 23 for three. They batted cautiously, adding an unbeaten 64 runs in 24.4 overs against accurate bowling, with some balls keeping low.
Tinashe Panyangara took two wickets for 12 runs in eight overs.
Tendai Chatara claimed the third wicket when Mohammad Hafeez drove a catch to short cover.
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Earlier, Pakistan off-spinner Saeed Ajmal took seven for 95 as Zimbabwe were bowled out for 327. Ajmal took all three Zimbabwe wickets that fell on Thursday as the host nation added 46 runs to their overnight 281 for seven.
Elton Chigumbura became the third Zimbabwe batsmen to score a half- century, making 69 before he was ninth out, caught off bat and pad at short leg by Azhar Ali after a 129-ball innings which included eight boundaries.
Overnight batsmen Chigumbura and Shingi Masakadza took their eighth wicket stand to 32 before Masakadza went back on his stumps and was leg before wicket to Ajmal for 14. Chigumbura played some attacking strokes as he added a further 17 with Panyangara before he was out.
It was Ajmal's eighth haul of five or more wickets in Tests. His best figures were seven for 55 against England in Dubai in January 2012.