The visitors controlled the opening 20 minutes, but undid all their good work in the space of a four-minute spell midway through the fist half.
Shrimps boss Sammy McIlroy would have been furious at the way Mark Bentley was left totally unmarked to head home Albert Jarrett's free-kick in the 21st minute.
And the game was as good as over three minutes later when Nicky Southall's clever reverse pass was dispatched into the bottom corner by Simeon Jackson.
Jackson then hit the post when it seemed easier to score, but the former Rushden & Diamonds striker did bag his second ten minutes before the break with an emphatic left-footed finish from the edge of the area.
The Gills eased off in the second half, but still found time for an extraordinary fourth in the shape of Southall's hopeful 45-yard punt 17 minutes from time, which went in with the aid of a deflection from David Artell.
Substitute Mark McCammon smashed in the fifth with ten minutes remaining to complete a superb victory for Mark Stimson's side.