Industry, retailers and the Commission have been fighting Germany's single-use deposit scheme since it came into operation on 1 January 2003.
While Germany's government won a series of domestic court cases contesting the scheme, it was faulted by the Commission for imposing a barrier to trade within the EU.
Following two judgments of the European Court of Justice, Germany reworked the deposit system and simplified the rules on the recovery of the deposit for consumers.
In deciding to close the case the Commission said on Friday that it considers that the rules applied are now in line with the EU's requirements on the free movement of goods and on packaging waste.
Under the applicable German "Verpackungsverordnung" (Packaging Order), a mandatory deposit is charged on mineral waters, beer, and all soft drinks typically sold in cans, plastic bottles and glass.
Initially container deposits were set at €1 for single-use bottles.
The sum was lowered when government reformed the system on 1 May 2006 to meet EU trade requirements.
In its infringement procedure, the Commission had argued that there was no functioning nation-wide take-back system at the time of the introduction of the programme.
Retailers were only required to accept the return of packaging of the exact type, shape and size they had in their own stock.
"This cumbersome legislation made it difficult to import beverages into Germany and constituted a barrier to trade in the internal market," the Commission argued.
One-way bottles can now be returned in principle in every shop selling beverages in packaging of the same material type.
"The Commission has closely monitored the recent changes, which entered into force on 1 May 2006, and has come to the conclusion that the new system is working properly and is also applied to imported products without any discrimination," the administrative body ruled.