On Wednesday, the retailer told Sapa that it usually reviewed all its merchandise on a regular basis - "be it bananas, bread or magazines".
"We looked at the faith-based category of magazines and found they were not selling," spokesperson Julian Novak said.
There had been "a lot of feedback" from customers following the withdrawal of the publications and Woolworths would put the magazines back on its shelves.
This would take "a couple of days".
However, the entire magazine category would be reviewed in the new year.
The magazines that had been withdrawn were Joy, Vision, Lig, Finesse and Lf.
Woolworths' response followed the release earlier on Wednesday of an open letter to Woolworths CEO Simon Susman, from Dr Isak Burger, president of the Apostolic Faith Mission of SA.
In the letter, Burger said he was "shocked that a store of Woolworths' reputation would resort to religious discrimination and perceived animosity towards the largest faith group in the country."
Burger and his family had taken a decision not to shop at Woolworths stores with immediate effect "as a result of Woolworths' perceived anti-Christian policies".
He encouraged other Christians within the ambit of his influence to support a nationwide boycott of all Woolworths stores until the "unfair policy" was reversed.
The Solidarity Helping Hand Women in Action also demanded Woolworths immediately reverse its decision to no longer sell Christian magazines.
"Women in Action’s reaction comes after editors of Christian magazines like Lig, Juig, Joy and Lf were informed that these magazines will no longer be sold at Woolworths."
The women's group said the announcement had unleashed a "storm" on social network Facebook, "where Christians from across South Africa are protesting against the decision.
"Afrikaans women comprise a big part of Woolworths’ support base," Dr Maryn Botha, national chairperson of Women in Action said.
"It is a crying shame that the needs of such a large portion of Woolworths’ traditional support base are not taken into account."