Which is the best university to pursue MS in civil engineering in Germany through scholarship?

Dear Sreesutha, very frankly there is no official ranking system therefor it really does not matter where you have studied in Germany. These are the leading ones RWTH Aachen, TU Berlin, TU Braunschweig, TU Darmstadt, TU Dresden, Leibniz Universität Hannover, KIT Karlsruhe, TU Munich and University S

I think, there is no option to get admission through scholarship.