The 23-year-old Edinburgh back, who was winning his fourth cap, was taken off following a sickening clash of heads with opposite number Andrew Trimble at the Aviva Stadium.
The incident occurred during the 62nd minute as Ireland scrambled furiously inside their own 22, with Jones collapsing instantly from the collision before receiving prompt medical attention.
An update on Scotland's official Twitter feed read: "Lee is going to hospital for a precautionary scan for his head knock.
"He remains alert and his parents are with him. Thanks for all concerns."
Jones is now likely to be a major doubt as Scotland travel to Italy next weekend seeking to end a run of six successive Test losses to avoid the wooden spoon.
Scotland head coach Andy Robinson said: "Lee's been taken to hospital with a head knock. We are concerned for him."
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