Ola Toivenen sent Sweden into a first-half lead in the Group F clash, but Marco Reus levelled the scores early in the second period before Kroos netted a winner for Germany in the fifth minute of added time at the end of the 90.
Germany have kept their World Cup destiny in their own hands ahead of their final group game with South Korea next week, and Low has hailed Kroos for bouncing back from an early mistake to make the difference late on.
"I was very pleased for Toni Kroos because he was involved in that mistake that led to their goal. But he did very well with the free-kick in the dying moments. I was very pleased he was able to turn his game around and score that vital goal," Low told reporters.
Kroos entered this summer's World Cup off the back of helping Real Madrid land their third successive Champions League title.