Barrow are now only out of the League Two drop zone on goal difference after another narrow home defeat.
A goal in the 13th minute of stoppage time gave Gillingham an overdue win after three successive defeats.
But for Barrow, it was a third loss in a row for new manager Dino Maamria and they are only ahead of Harrogate through their superior goal difference.
The large part of the added time at the end of the game was down to an injury to home forward Jovan Malcolm who was down for eight minutes receiving treatment for a leg injury.
It was a last gasp winner from Robbie McKenzie as he forced home that late corner from Lenni Cirino to send the Gills home to Kent with the points.
Overall, the visitors just about deserved the win, their first at Holker Street for almost 60 years when they met in the old Third Division.
Both sides had struck the woodwork – Ronan Hale beating home keeper Wyll Stanmway after 47 minutes but seeing his effort come back off a post.
Barrow were closest to nosing ahead on 88 minutes when Charlie McCann struck the bar direct from a corner.
