The Australian believes his side showed admirable fight to still be in the game after the disappointment of being rolled over for 49 in their first innings on Saturday, their lowest test score.
Pakistan still need 297 runs to win the test with six second innings wickets remaining, but a century stand from captain Misbah-ul-Haq (44 not out) and Asad Shafiq (53 not out) on day three has given them hope.
"Whatever happens from here, today should give all the players confidence for the remaining two test matches in Cape Town and Centurion," Whatmore told reporters on Sunday.
"I thought the wicket settled down a bit too and what we wanted to do today was show better application. We did that and the players will have learnt a lot from this experience. Nine of our 11 for this test have never played in South Africa with the red ball and so it is a big learning curve."
Whatmore also said he had a few words with debutant Nasir Jamshed after the opener fell attempting an ambitious pull shot.
"He has been with our ODI team ever since I have been in charge and so you forget this is his test debut. But I was not happy with him and told him so," he said.
South Africa are favourites to complete a win on Monday but with rain predicted for the final few days of the test, all three results remain possible.
Wicketkeeper AB de Villiers, who earlier hit his 15th test century, says the new ball due five overs into the fourth day will be crucial.
"The wicket is playing better, the ball is not going around as much as it was on the first two days," he said. "But we have a new ball coming up tomorrow and we hope that will speed things up a bit.
"Pakistan will be looking to get through the new ball and then from 20-30 overs start to be positive again. We will be aware of that."