The striker played a key role with a goal and an assist in the Bees' 2-0 victory at the London Stadium, a result that has heaped pressure on Hammers' boss David Moyes.
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But for Toney, things didn't look too promising as he looked in considerable discomfort on the turf.
Rising for an aerial duel, the striker appeared to fall awkwardly on his right knee before lying on the pitch for several minutes.
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After receiving treatment, Toney was then stretchered off the pitch, and was replaced by defender Pontus Jansson for the final moments of the match.
It remains to be seen how severe the injury will prove to be, but Brentford boss Thomas Frank is hopeful that it's nothing serious.
Frank told talkSPORT: "I don't know too much about it. It's unusual Ivan wanted to be subbed off, he's very resilient and can take a lot of pain.
"Of course I worry a bit but also you know with these things we need to assess it for the next couple of days and see how it goes.
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"There's a chance it's nothing serious but we don't know."