The 32-year-old Yousuf led the hosts to 225 for four, 19 runs ahead of the tourists, confirming his liking for the Gaddafi stadium where he has scored hundreds in his previous three tests.
West Indies were bowled out for 206 in 56.1 overs on the first day.
The home side did not lose any wicket in the second session after resuming on 141 for four, Yousuf adding 85 runs with Shoaib Malik who was unbeaten on 39 at the interval.
Yousuf, in his 71st test, was very fortunate to survive a stumping appeal against left-arm spinner Dave Mohammad with his score on 53.
Television replays suggested his foot was on the line, but Sri Lankan umpire Asoka de Silva surprisingly did not refer the decision to the third umpire.
Yousuf was also dropped on 43 by Daren Ganga off Jerome Taylor just before lunch but otherwise he played a spectacular innings, stroking the ball sweetly despite some movement and turn in the pitch.
His innings of 93 from 166 balls included flowing cover drives off the seamers and cut shots to the spinners as he hit 12 fours.
Malik stroked five fours and one six as the pair took 203 balls to compile their undefeated fifth wicket stand.
Pakistan had lost Younis Khan (11), Mohammad Hafeez (57) and captain Inzamam-ul-Haq for his 15th duck in 114 tests before lunch to give West Indies hope.