The big-serving American has been hampered all week by what he described earlier in the week as "a bit of tendonitis".
He was due to play Spain's Fernando Verdasco in the first match of today's day session. However, following Isner's withdrawal Verdasco was awarded the match 6-0 6-0.
Speaking on court, Isner said: "I'm very, very sorry to all the fans here, I really wanted to play here against Fernando, so I apologise for that and I hope you guys understand."
As a result, Spain progress to Saturday's final as the top-placed team from Group B.