The winger has suffered a stress fracture in the base of his spine – just 13 days after arriving permanently.
He now joins fellow left-sided player Niko Kranjcar on the sidelines, who is recovering from rupturing ankle ligaments while on duty for Croatia.
The former Dinamo Zagreb star last week underwent an operation and is expected to return in late November.
Thomas will be assessed in three weeks' time before the decision is made whether to operate.
It's a long-term absence and a double blow for Harry Redknapp, with both players out of the UEFA Cup first-round clash with Vitoria Guimaraes.
Even if the Blues qualify, the duo face a battle to feature in the second-round group stages, which start on October 23.
For Thomas, the news comes at a time when he had begun to catch the eye on the south coast.
The ex-Arsenal winger impressed from the substitutes' bench against Manchester United last week on his Fratton Park debut.
Initially, concerns over his back problem had prompted a fitness test before the match, one which he passed.
Thomas has not trained since and, following a visit to a Havant specialist on Monday night, is hoping to avoid going under the surgeon's knife.
But Redknapp admitted it was another blow to an already threadbare midfield.
He said: 'Jerome is out for 12 weeks, which is another big blow for us.
'We're not quite sure when it happened, probably the day before the Manchester United game in training.
'At the time he complained a bit but wanted to play so much and passed a fitness test. He did well in that game, too.
'Now it looks as though he could need an operation to get it sorted, which is really disappointing for all of us.
'The lad gives you something different, he's got pace, can run at players and cause defences all sorts of problems.
'With Niko also out for quite a long time it leaves us a bit short on the left there.'
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The full article contains 382 words and appears in The News newspaper.