But they made desperately hard work of overcoming a Gillingham side without an away win for 10 months.
Barnsley wasted a string of excellent chances and were also dealt a hat-trick of injury blows.
Defender Robbie Williams and winger Martin Devaney both limped off in the first half, while recent recruit Tommy Wright was also forced to withdraw with a knock 15 minutes from time.
The home side did start brightly and Wright, preferred in the starting line-up to fellow frontman Marc Richards, spurned a glorious second minute chance.
Wright was clean through but his shot was tame and was easily saved by Jason Brown.
Two minutes later Wright did have the ball in the Gills net only for his header to be ruled out for an apparent foul on Brent Sancho.
But Barnsley did make the breakthrough on 15 minutes, Shuker showing his strikers the way to goal with a rising drive from just inside the box.
Gillingham had a couple of decent openings themselves but full-back Sean Clohessy drove over the top and then Darren Byfield's header went straight at Barnsley keeper Nick Colgan.
The home side had to change formation following Williams' injury with striker Paul Hayes being asked to operate at left wing-back.
The home side continued to miss openings, however, with substitute Richards spurning a great chance with a free header from 12 yards.
Gillingham applied late pressure by piling high balls into the Barnsley box but the hosts hung on for a vital victory.