Jones has been out of action since the 0-0 draw with Hull earlier this month.
While Rooney and Carrick were both on the bench for the 2-0 win over Watford on Saturday.
Jose Mourinho has revealed Phil Jones, Wayne Rooney and Michael Carrick are all injured
But all three missed Manchester United training earlier today.
And Mourinho has confirmed they will all miss the round-of-32 Europa League clash with the French club.
“Phil is still recovering from the injury of the Hull match," Mourinho said.
Manchester United line-up predicted to face Saint-Etienne
Mon, February 13, 2017
Express Sport predicts who will start for Jose Mourinho's Manchester United side against Saint-Etienne in the Europa League on Thursday (8.05pm)
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How will Manchester United line up against Saint-Etienne on Thursday?
Phil Jones will miss the clash with St Etienne
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"Wayne and Carrick, I don’t want to say injuries, because we are speaking about little muscular problems and protection of these problems.
"So all three out tomorrow.
"Apart from that everything is right.”