MOSCOW—German Chancellor Angela Merkel confronted Russian President Vladimir Putin at the Kremlin over the Ukraine crisis, balancing a tribute to Soviet losses in World War II with a rebuke of Russia’s policies today.

Ms. Merkel flew to the Russian capital Sunday, a day after skipping Moscow’s vast military parade in honor of the 70th anniversary of the defeat of Nazi Germany. She joined Mr. Putin at a military wreath-laying ceremony at the Tomb of the Unknown Soldier outside the Kremlin wall, walking behind slow-marching...