The win helped Germany maintain its flawless record of seven straight wins on the road to Russian Federation which leaves them five points clear of nearest rivals Northern Ireland in Group C with three games left.
Timo Werner latched on to Mesut Ozil's fine pass to give Group C leaders Germany a fourth-minute lead, but Vladimir Darida levelled for the hosts with a 25-yard effort 12 minutes from time.
Kroos floated an inviting free-kick into the box and Hummels got up highest to power in a header that ensures Germany move a step closer to World Cup qualification ahead of Monday's home game against Norway.
Germany could qualify for the World Cup on the same day if they beat Norway at home and the Irish fail to beat the Czechs.
"Of course, we can not be satisfied with the way we played", said Germany coach Joachim Loew.
"We can't be happy with the way we played", said Loew. Germany's success has been a solid team effort and this should be another win heading into the 2018 World Cup. Mueller, Germany's captain for the night with Manuel Neuer just back from a fractured foot, was also highly critical. "The Czech Republic defended well, but we made life hard for ourselves". Michael Krmencik fired over after trying to lob Barcelona goalkeeper Marc-Andre ter Stegen in the German goal. The Czechs were clearly the best team in the second half.
Bayern defender, Mats Hummels headed in the victor in the 88th minute, keeping Germany at the top of the table.