Febian Brandy starred on his Gillingham debut as they gained revenge for last week's league defeat by Southend by beating them in the FA Cup first round.
Brandy, on loan from Manchester United, was hauled down by Adam Barrett early on but Simeon Jackson's weak penalty was easily saved by Steve Mildenhall.
But Brandy set up Curtis Weston to open the scoring, before netting himself when he converted Chris Palmer's cross.
Mark Bentley sealed their second-round place by heading in Palmer's centre.
Gillingham manager Mark Stimson told BBC Radio Kent:
"We should have been a goal up before our first goal with the (missed) penalty.
"Overall thoroughly deserved, but we shouldn't have lost last week to be honest.
"I would prefer to win today for the prize money and if we get another decent tie, then there's more money there."
Southend United manager Steve Tilson told BBC Essex:
"We were just a little naïve today, I bet over the 90 minutes we had as many chances as them.
"If we look at the stats and go over the game again we had many more chances than them, but we haven't taken them."
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