Harmison had hoped to play for Durham in their first final appearance in English domestic cricket's one-day competition, after missing the entire Test series against India.
The paceman, 28, has only recently recovered from a hernia operation.
He complained of soreness in his back during the current County Championship clash with Surrey earlier this week.
Harmison has had two scans, which identified internal bleeding in his back thought to be related to a muscle injury.
It is not currently known when he will return to action, Durham said, though the likelihood is he will miss most of the rest of the English season.
"The severity of the injury has surprised everyone and the timing couldn't be worse," said Harmison.
"Having played for Durham through the lean years I was looking forward to making my mark in Durham's first ever final and I'm heartbroken I won't be playing.
"However, we have a strong squad and whoever steps up to take my place will be a quality player.
"It doesn't matter which 11 players we put out at Lord's. We have a good chance of bringing the trophy back to Durham and I'll be in London with the team to give them any help they need."
Durham head coach Geoff Cook added: "Everyone is devastated for Stephen. He has worked so hard to come back from his operation and was looking forward to playing at Lord's.
"This is a cruel blow for him but when one door closes another one opens and this is a real opportunity for another one of our talented squad."
It has been a disjointed domestic season for Harmison, who struggled for form early on and then attempted to delay surgery on his troublesome hernia to get through the three-Test campaign against India.
Despite playing for a couple of weeks after first experiencing discomfort during the fourth Test win over West Indies at Durham's Chester-le-Street home, Harmison suffered a recurrence of the problem on the eve of the Lord's opener against India.
Yet he was back on the field for Durham as captain just three weeks after undergoing surgery, captaining the side against Sri Lanka A, in his bid to get fit for Saturday's showpiece match.
Harmison, who has retired from international one-day cricket, has three months until his next potential international commitment -- England's Test tour of Sri Lanka which begins on November 14.