It said that the agency that stripped France and Austria of their AAA status wrongly took the EU debt crisis response as being only about austerity.
The Commission also said that it was "encouraging" EU governments to ban the ratings agencies from passing judgment on countries under bail-out and reform programmes.
Senior economic spokesman Olivier Bailly said the idea that Europe was "pushing a strategy based on the perspective of fiscal austerity alone was a serious misperception".
He said EU leaders, who will meet at a summit on 30 January to agree a pact calling for balanced government budgets, were working on a "twin strategy based on smart consolidation and structural reforms".
Mr Bailly said moves to boost growth and employment were "being implemented and now delivering results".
As a result, he said S&P's decision to downgrade nine of the 17 eurozone nations, was "very odd as far as the timing was concerned".
He accused the ratings agencies of taking decisions without being in possession of the full facts, citing monthly updates on "exact" public finances shared among EU capitals "on a confidential basis".
Meanwhile, European share values remain largely unaffected this afternoon by the downgrade.
Elsewhere, EU Commissioner for the Internal Market Michel Barnier has said the euro is here to stay as a global currency and the eurozone will bounce back from its debt crisis.
Mr Barnier said: "Let there be no mistake: this is not a crisis of the euro as a currency.
"The euro is here to stay. In the last ten years the euro has proven itself as a true world currency ... and despite the difficulties, it remains strong."
He said the real crisis the eurozone faces right now is a crisis of confidence.
Our political unity and our determination and our ability to rectify what is wrong are being tested, he added.
S&P's downgrades EFSF
Standard & Poor's has downgraded the EU's bail-out fund, the European Financial Stability Facility (EFSF) from AAA to AA+.
The move was not unexpected following the agency's downgrade of nine euro zone countries' debt ratings - including those of AAA-rated France and Austria - on Friday.
The fund's director, Klaus Regling, said the fund would retain its effective lending capacity of €440 billion despite S&P's decision.
The EFSF was set up in May 2010 and has so far been used to bail out Ireland and Portugal. The S&P move could increase its borrowing costs, although some analysts believe the bond markets had already anticipated the decision.
