Brighton took full advantage and all three points in the relegation scrap as striker Leon Knight bagged his first of the season, after he was brought down by Chris Hope.
The Gills got what they deserved after the dismal first-half performance, when their three strikers could not manage a single attempt on goal.
Patrick Agyemang, who is playing behind the two front men has pace and power but not the guile to link midfield to the attack.
In contrast Brighton linked together quickly on the counter attack should have had a penalty after six minutes, when Gillingham goalkeeper Steve Banks clearly brought down Alexis Nicolas.
Knight then had a clear opportunity on goal when he ran clear but Banks managed to save his shot one handed.
Knight continued to hunt for the first goal and managed to latch on to a deflected Adam Virgo free-kick, but Banks got down quickly to save his low effort.
The lively Brighton front-man then turned provider with a superb cross-field ball which picked out Dean Hammond, but his low shot was smothered by Banks.
Perhaps out of sympathy Brighton goalkeeper Michels Kuipers almost gifted the Gills a goal when his clearance hit Nicky Southall, but bounced away from goal.
A second Gillingham chance came from a second Brighton mistake when a miscued clearance allowed substitute Mamady Sidibe to race clear, but he was tackled before he could pull the trigger.
After going behind Darren Byfield summed up Gillingham's performance when he skied a close-range free-kick to spurn the best chance of an equaliser.