James Collins' early strike put the visitors ahead before a Liam Lawrence own goal restored parity on the half-hour mark.
But Barnett's 32nd-minute effort consigned Rovers to a third straight defeat at the hands of League One opposition in round one of the competition.
Rovers handed a debut to 17-year-old Ryan Nyambe, but his poor pass led to a ninth-minute opening goal. Abu Ogogo latched onto the ball and, although his shot was saved, Collins fired in the rebound.
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Blackburn goalkeeper Jason Steele was lucky not to concede a penalty when he appeared to clip Ogogo, but the hosts were level on the half-hour as Nyambe's cross was diverted into his own net by Lawrence.
Parity lasted for only two minutes, though, as a clearance fell to Barnett 20 yards out and he drilled emphatically into the bottom-right corner.
Shrewsbury goalkeeper Jayson Leutwiler acrobatically palmed a 30-yard Ben Marshall effort behind on the stroke of half-time, while early in the second period Collins blazed over from close range after the ball had fallen kindly to him.
Blackburn substitute Fode Koita then saw a close-range header tipped over and went even closer in the final minute when his header drifted agonisingly wide as Rovers bowed out.
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