The Toffees full-back seemed to land on his neck after jumping for an aerial ball with Lyon attacker Maxwel Cornet and required serious medical attention as he lay still by the corner flag.
Around 10 medics tended to the Curacao international, who was making his first appearance since the reverse fixture against Lyon a fortnight ago, and he will now spend the night in a nearby hospital as his Everton teammates trudge off home after suffering yet another damning defeat which ended their dreadful Europa League campaign.
Martina was treated on the pitch for around eight minutes and required a neck brace as he left the ground on a stretcher. A brief statement from Everton read: "Cuco Martina has been taken to hospital and will be observed overnight. We wish him a swift recovery."
Everton interim boss David Unsworth also provided an update on Martina in his post-match press conference: "Cuco was concussed & complaining of pains down his neck. He's gone straight to hospital for X-rays & scans. We wish him all the best."
There were some suggestions that Martina was not able to feel his legs after the incident, but Unsworth did know if that was the case: "Not too sure. He's in the best hands now at hospital and all the right tests will be made."
Muhamed Besic came on to replace Martina in the first half with the scores level, but a second half capitulation allowed Bertrand Traore, Houssem Auoar and Memphis Depay to condemn Everton to their fifth consecutive defeat.
The result at the Stade de Lyon ended Everton's dismal time in Europe, which is shaping up to be the worst in the history of the competition, and all but ended caretaker manager Unsworth's hopes of succeeding Ronald Koeman on a permanent basis.
Unsworth has overseen three defeats during his brief reign in charge of Everton, and knows his side must emerge victorious against Watford on Sunday in order to arrest a worrying slide that has seen them slip into the relegation zone and exit the Europa League and Carabao Cup.
"No excuse," Unsworth said. We can't defend the way we did and expect to win a game. We now have a massive game. A must win game."
"We can't cave in the way we do when we concede a goal. We need to rectify that very, very quickly."
'Rhino' was also quizzed about the impact the damning defeat had on his chances of being appointed Everton manager on a permanent basis, but was unsurprisingly in no mood to digress about his future.
"It's not about me. It's about the football club. It's about getting over this disappointing result," said Unsworth.
"Sunday is a huge game for me, huge game for the club and I've left the players in no uncertain terms that it's a huge game for them."