The EU executive said Germany appeared legally justified in reimposing border controls on Sunday, especially on its Austrian frontier, and said it showed the need for EU states to agree a common approach to refugees.
"The temporary reintroduction of border controls between member states is an exceptional possibility explicitly foreseen in and regulated by the Schengen Borders Code, in case of a crisis situation," the European Commission said in a statement.
"The current situation in Germany, prima facie, appears to be a situation covered by the rules."
It added that the executive would keep the situation under review and said the aim would be to return to the normal situation of no border checks between member states of the Schengen zone "as soon as feasible".
"The German decision of today underlines the urgency to agree on the measures proposed by the European Commission in order to manage the refugee crisis," the Commission said.
Commission President Jean-Claude Juncker, who spoke to German Chancellor Angela Merkel shortly before her government made the decision public, has been pressing reluctant east European governments to support Commission proposals, which Germany backs, to redistribute asylum-seekers around Europe.
Juncker also spoke to the Hungarian, Czech and Slovak leaders on Sunday, seeking to break their collective resistance to his plans before EU interior ministers debate them at an emergency meeting in Brussels on Monday.
Among arguments EU, German and other officials have used to pressure leaders who say their societies cannot take in large numbers of immigrants have been warnings that a failure to fix a common plan on migration could wreck the Schengen open borders system which is especially valued in formerly Communist states.
"The free movement of people under Schengen is a unique symbol of European integration," the Commission statement said.
"However, the other side of the coin is a better joint management of our external borders and more solidarity in coping with the refugee crisis. This is why Monday's extraordinary council of interior ministers is so important. We need swift progress on the Commission's proposals now."