The project, by researchers from the Planetary Science Institute in Arizona and the Georgia Institute of Technology, identified the clay minerals using a spectroscopic analysis from the Mars Reconnaissance Orbiter.
The research found that clay also exists in the Meridiani plains that Opportunity rolled over as it trekked toward its current position.
Opportunity landed at Eagle crater in 2004 and only detected acidic sulfates. The rover has since driven about 35 kilometres to Endeavour Crater, an area of the planet Wray pinpointed for clays in 2009.
"It's not a surprise that Opportunity didn't find clays while exploring. We didn't know they existed on Mars until after the rover arrived. Opportunity doesn't have the same tools that have proven so effective for detecting clays from orbit," said researcher James Wary in a statement.
The clay signatures near Eagle crater are very weak, especially compared to those along the rim and inside Endeavour crater.
Wray believes clays could have been more plentiful in the past, but Mars' volcanic, acidic history has probably eliminated some of them.
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"It was also surprising to find clays in geologically younger terrain than the sulfates," said Eldar Noe Dobrea of the Planetary Science Institute.
Current theories of Martian geological history suggest that clays, a product of aqueous alteration, actually formed early on when the planet's waters were more alkaline.
As the water acidified due to volcanism, the dominant alteration mineralogy became sulfates.
"This forces us to rethink our current hypotheses of the history of water on Mars," he added.
Even though Opportunity has reached an area believed to contain rich clay deposits, the odds are still stacked against it. Opportunity was supposed to survive for only three months.
It's still going strong nine years later, but the rover's two mineralogical instruments don't work anymore. Instead, Opportunity must take pictures of rocks with its panoramic camera and analyse targets with a spectrometer to try and determine the composition of rock layers.
"So far, we've only been able to identify areas of clay deposits from orbit. If Opportunity can find a sample and give us a closer look, we should be able to determine how the rock was formed, such as in a deep lake, shallow pond or volcanic system," said Wray.
The study is published in the journal Geophysical Research Letters.