The 21-year-old, brought on 55 minutes into Saturday's straightforward 7-0 win in Nuremberg, was given unfavourable treatment due to a dive for his club side against Schalke 04 last December.
Werner later apologised for the incident, which helped his side to a 2-1 Bundesliga win, and Low insists that it is now time for those in the stands to move on.
"There was a dive once, he made a mistake, and he admitted he was wrong," he told Bild. "But we are talking about a very young player here.
"Someone who plays for the national team, is only at the start of his career and who has scored 21 goals in one season in the Bundesliga should not be jeered and whistled. That is simply not okay."
Werner, who puts the bad reception he receives down to simply playing for controversial club Leipzig, is reportedly on the radar of Premier League side Liverpool.