The usually reliable Steyn only landed one goal from his six attempts. He has scored 486 points in 41 tests for the Springboks but was off target at the Forsyth Barr Stadium.
"The guys opted to give Morne one more chance," captain Jean de Villiers said after the game.
"You have to show confidence in your players as well but at times you have to make the difficult decisions."
The change was made soon after Steyn failed to convert Bryan Habana's second-half try. Coach Heyneke Meyer had delayed replacing Steyn with rookie Johan Goosen (20) earlier, because Goosen had not played much rugby in the last three months.
Meyer believed Steyn's goal-kicking woes stemmed from playing with a different ball.
"We use the Gilbert ball in Super rugby and in South Africa but we played with the Adidas ball in the test," Meyer said.
"We saw goal kickers struggle in the World Cup as well."
Meyer said the attack on All Black captain Richie McCaw by Dean Greyling was unacceptable.
"We pride ourselves on our discipline. I have apologised to Richie. We don't condone it and I think his yellow card cost us the game.
"We never condone playing dirty. Lack of discipline is non-negotiable for us. We will view the video and if he is in the wrong, we will take action internally against him."
Meyer is adamant that the Springboks had the correct game plan for the All Blacks.
"We put the All Blacks under a lot of pressure in the first half," he said. "But we did not turn that pressure into points.
"The big difference between the two sides was that whenever the All Blacks put pressure on us, they got points, and we didn't."
The coach praised the brilliant individual try scored by Habana early in the second spell.
"He is a game-breaker and scored a try out of nothing. We couldn't ask for more. He has come back to form after having a bad patch a year ago."
Flanker Francois Louw, who returned from the Bath club in England three weeks ago to join the Springboks, played a key role by carrying the ball up field, and helping South Africa win 74 rucks and mauls.
"A test match like this comes down to executing the opportunities you get. We had a few of them but we didn't quite pull them off," Louw said.
"In test match rugby you have got to take them or you will come off second best."
Winger Francois Hougaard said it was the third game in a row South Africa should have won.
"We made stupid mistakes and let it slip," Hougaard said. "We can't make any excuses for that any more. We had our opportunities but just didn't use them."
