Kroos, 28, scored a spectacular free-kick in the 95th minute to secure the World Champions a crucial victory to keep them in contention to defend their title.
The European giants looked set for an early elimination as Sweden frustrated them for large spells of the encounter with some resolute defending.
But the Real Madrid midfielder's winning strike sparked wild scenes - that eventually marred a spectacular end to the Group F encounter.
Janne Andersson, the Sweden coach, accused Germany of 'rubbing it in our faces', for which the German FA apologised - while FIFA has also opened an investigation over the alleged provocative behavior of Kroos and his teammates.
"It makes me feel like it's much more fun for people to write badly about us," he said, as quoted by The Telegraph. "We get no help from all those who write, analyse, accuse us of bad body language.
"But nobody will write us a title. It all has to come from us. With that sort of fighting spirit, we deserve to reach the final."