AJ Leitch-Smith opened the scoring, latching onto Ben Purkiss' cross-field pass to lash his 12th goal of the season into the top corner.
Carl Dickinson added a second before Richard Duffy cleared off the line after Vale keeper Jak Alnwick spilled Bradley Dack's shot.
The Gills remain in sixth but are just two points above Barnsley in seventh.
Gillingham's play-off hopes were dented as their winless run extended to four games with defeat by Port Vale.