The Venezuela international and reigning MLS MVP landed awkwardly after colliding with a team-mate before he was substituted in the 79th minute at Mercedes-Benz Field.
It sent shockwaves around Atlanta, where Martinez has scored 26 goals to help the titleholders up to third in the Eastern Conference in their pursuit of back-to-back MLS championships.
Asked about Martinez post-match, De Boer told reporters: "I'm afraid that he has something serious, but we have to wait. They're evaluating him now."
"Probably tomorrow we can have a better diagnosis and then we have to make our plan," the former Inter and Crystal Palace boss said. "Hopefully it's not so bad. But I can't say if it's good or bad. I don't know.
"We know Josef a little bit -- he's a tough guy. He will not suddenly step off the field. He will have something, that's for sure. But we have to wait. It's too early to predict.
"But I think it's not a good sign that he goes off ... but it's like that. We have to deal with it. Again, we have to wait."
Goals from Justin Meram, Emerson Hyndman and Gonzalo Martinez saw Atlanta clinch a home play-off match.