Trainer Brian Meehan said that the Zebedee colt sustained the injury when winning the Richmond Stakes at Goodwood last month.
The Manton handler had hoped to have his charge back on song for the Middle Park Stakes at Newmarket on September 30, but has now opted to draw stumps with next year in mind.
A statement posted on www.brianmeehan.com read: "Barraquero is out for the rest of the season.
"He suffered a small fissure in his shin which he sustained in the Richmond which has proved difficult to heal while trying to prepare him for the Middle Park.
"Whilst it is a minor injury, it does require some time off to heal properly, therefore he will not run again this season.
"He will now enjoy the winter off and be prepared for the Guineas next year."
Barraquero was also a six-length winner of a novice event at Chepstow in July and is a general 33-1 shot for next year's 2000 Guineas.