The problem first surfaced in the 67th minute when Courtois went down after a routine passage of play and signalled to the bench for treatment. Referee Michael Oliver called the hydration break, and Courtois initially returned to action afterwards, appearing to have shaken off the issue.
Within a few minutes, though, the discomfort worsened and he was replaced by Senne Lammens in the 72nd minute, leaving the pitch visibly emotional after trying to play on.
Speaking afterwards on DAZN, Courtois explained how the injury developed.
"On a long kick I felt something, nothing more, I thought my hamstring was tight because I'd taken 30 long balls," he said. "I noticed it a little on some saves, and on another long kick I felt it getting worse.
"I sat down for a moment so the doctor could look at it and I wanted to carry on, but I couldn't strike the ball properly, and the manager told me that if I wasn't at 100% he'd sub me off. If the manager wants someone at 100%, that's no problem."
Asked about his Belgium future, Courtois was noncommittal.
"As for my future with the national team, well, we'll see," he said. "I might like to take a break from the Nations League, since it's not the most important thing, and maybe come back for the European Championship qualifiers. But in the end it's a decision the federation has to make. If not, then maybe today was my last match."
Reflecting on the game, in which Belgium led before eventually losing 2-1, Courtois said: "It's bad luck that the rebound fell to Fabian, in the second half they had more chances. I felt good with the saves, with the balls in behind, Lamine's crosses. I felt it was going to be very hard to get a second goal past me."
He was also quick to defend Lammens, whose fumble led directly to Mikel Merino's winner.
"It's true the pitch is very dry, it's bad luck, in the end that's football. You shouldn't crucify the lad, he's a great goalkeeper, he's had a great season at United and he doesn't deserve this."
On Belgium's wider tournament, he added: "When we played against Egypt, Iran defended with eleven behind the ball, and then New Zealand, Senegal and the United States. Scoring a goal against Spain has its merit, we needed to do something more."
Courtois closed by turning his attention to Real Madrid, where he will link up with new head coach Jose Mourinho once the injury has been assessed.
"Really looking forward to that with a lot of excitement," he said. "First I need to wait and hope the scan doesn't show anything serious, which I don't think it will. I'm hoping to be perfect by the middle of August to start the season."