South Africa swept Pakistan 3-0 in the Test series but Misbah's team proved tougher opposition in the one-day series before losing it 3-2.
Misbah says his players benefited from "playing tough cricket in tough South African conditions as you mentally get more focused" for difficult conditions.
The team's six-day training camp ended on Wednesday in the northern town of Abbottabad where former captains Wasim Akram and Javed Miandad talked to the players.
Pakistan will play two ODIs each against Scotland and Ireland later this month before taking on West Indies, South Africa and India in its Champions Trophy Group B matches.