The 30-year-old scored 109 in the tourists' total of 467 against the Patron's XI, which also included Hasim Amla's 87, Jacques Kallis's 73 and an equally sparkling 81 from AB de Villiers.
In reply, the Patron's XI were 136-3 at the close of the second day of the three-day match.
Taufiq Umar, recalled for the first Test, was dismsissed for 50 while Shahid Yousuf made 42 and Babar Naeem 22 on a day when it was all about South Africa's top order.
Boucher, who hit nine boundaries and a six, added 118 for the sixth wicket with de Villiers and another 58 with Andre Nel (14), frustrating the home team's attack.
De Villiers was unlucky to miss his century, edging to slip. He hit eight boundaries in his 233-minute stay at the crease.
Leg-spinner Rizwan Ahmed returned figures of 7-144 but his bowling did not deter the tourists as he had little support from the other end on a placid wicket offering little for the bowlers.
Boucher, who reached his fifty off 121 balls, paced his innings in the afternoon, flicking Ahmed for a couple to reach his well-deserved hundred in nearly four hours.
Ahmed then mopped up the lower order, dismissing Morne Morkel (seven), Nel and Paul Harris (four) before another leg-spinner, Mansoor Amjad, dismissed Makhaya Ntini for nought to wrap up the innings.