Neil Harris opened the scoring four minutes before half-time and Matt Jarvis then stole the show with a fine brace in the second half.
Vale were infuriated though with a ninth minute incident after Craig James had blocked a Jarvis cross.
Rather harshly the linesman flagged for handball and the referee awarded a penalty - a decision which caused half a dozen Vale players to surround the officials.
Vale captain Tony Dinning was particularly vocal in his protests and was shown a yellow card before continuing his arguments and receiving a straight red card.
Play resumed in the 11th minute and there was the matter of Gillingham's penalty kick.
Tom Williams stepped up and struck Mark Goodlad's left-hand post, although that was still no consolation for Vale boss Martin Foyle who was sent to the stands after continuing to complain about the penalty decision and Dinning's subsequent red card.
Gillingham put the penalty miss behind them and went on to take the lead in the 41st minute.
A long ball from Ian Cox was played up to Williams, he flicked the ball into Harris' path and he did the rest, letting fly with a sensational 20-yard half-volley which flew into the net off the inside of Goodlad's left-hand post.
Gills doubled their advantage on 66 minutes when Jarvis, who had switched flanks, cut in from the left and scored with a sweet swerving shot.
And he wrapped it up eight minutes from time with a carbon copy of his first goal.
They were both clinical finishes and Gillingham were worthy winners.