The crisis saw the profits of top EU companies fall by 21% last year, according to the Commission's R&D scoreboard, published on Tuesday.
But despite this, the amount European firms invested in R&D only fell by 2.6%, significantly less than the 5.1% drop of US companies, the Commission said.
Meanwhile, the worldwide reduction was just 1.9%, largely thanks to growth in the Asian 'tiger' economies.
The scoreboard ranked the world's top 1,400 companies according to investment dedicated to R&D, 400 of which were registered in the EU in 2009.
"The wide gap with the top US companies (in hi-tech sectors) and the continuing rapid rise of Asian-based companies highlight the innovation emergency Europe is facing," she warned, calling on heads of state to set aside budgets for buying innovative products and services.
At present, no EU member state devotes more than 1% of its GDP to funding public or business research activities, according to the Commission.
However, Geoghegan-Quinn highlighted the common ground between its views and those of big European companies, noting that "major EU firms have largely maintained their R&D investment, showing that they recognise R&D as key to emerging stronger from the crisis".
Carmaker Volkswagen, for example, was singled out in the scoreboard as being the top R&D investor in the EU, despite the automobile sector suffering its worst sales figures for over a decade.
"EU investment has shown to have resisted the crisis better despite sectors being badly hit," a Commission spokesman underlined.
But R&D intensity in the Union remains low in key sectors determining future competitiveness, such as semiconductors, software and biotechnology, the study showed, and only two member states currently meet the Europe 2020 strategy's goal of investing 3% of GDP in research.
Whilst government-funded R&D has been reduced in past years in other economic powerhouses, investment from business sources compensates for this to a greater extent than in the EU, according to the scoreboard.
Sporadic picture across EU market
The pattern of R&D investment in the EU varies greatly amongst member states. Whilst R&D was down in France by 4.5% due to its large automobile industry, it fell by 6.6% in Sweden, where IT hardware is a major sector.
Meanwhile, Spain's R&D rocketed by 15.4% following growth in its telecoms and banking sectors.
Less EU companies – especially newly-formed ones – can be found in R&D-intensive sectors such as biotechnology, explaining the overall difference in investment compared with the US, experts say.
Others pointed out that the scoreboard takes into account R&D investment undertaken by companies registered in a given country, whereas the EU's 3% of GDP target refers to overall investments in that country. So, Latvia for example could appear to be investing a lot according to the EU measure, when the high score is actually due to investments by foreign firms.
Galileo bucks the trend
On a more positive note for the EU, Galileo, the EU's flagship satellite project to rival the US global positioning system (GPS), saw a different turn in fortunes.
On the same day of the scoreboard's publication, the European Space Agency signed a contract with industry worth €194 million, seen as a major step in making the project a reality.
The fully deployed system will consist of 30 satellites using the latest technology and is expected to generate "tens of billions of macro-economic benefits" and "thousands of jobs" through the additional services it will be able to launch in 2014, according to the Commission.