Middlesbrough earned their fourth successive away win - in manager Tony Mowbray's 100th match in charge.
Striker Emnes enjoyed a fair slice of good fortune in notching his fourth goal of the campaign, his 21st-minute effort from the edge of the penalty area taking a wicked deflection to wrong-foot Brighton's Polish international keeper Tomasz Kuszczak.
It proved to be the only goal of the game as Middlesbrough extended their impressive record against the Seagulls to 10 matches in all competitions.
In contrast Gus Poyet's men have tumbled from their lofty early-season heights. They topped the Championship after a five-match winning sequence, but have now taken just two points from a possible 12.
Yet they will feel they should have drawn level just after the hour mark. A shot from Moreno David Lopez was bravely blocked by Jonathan Woodgate, outstanding Boro keeper Jason Steele then kept out a header from Ashley Barnes, before Craig Mackail-Smith sent his header from six yards over the top instead of into the back of the net.
Brighton had also enjoyed most of the possession in the early stages of the game at the Amex Stadium. That was mainly down to mistakes in Boro's midfield, with stray passes from Nicky Bailey and Josh McEachran, but Grant Leadbitter produced a good tackle inside the penalty area to deny a clear chance for Mackail-Smith.
But Boro looked dangerous on the counter-attack and Dutch attacker Emnes silenced the home crowd by making the breakthrough.
Brighton tried to hit back and in the 28th minute an outswinging corner from the left by Lopez was met by Dean Hammond but his header from six yards flew over the crossbar.
Two minutes later striker Craig Mackail-Smith latched onto a low ball sent in from the left but his 12 yard shot was superbly turned over the top by Steele.
The Seagulls kept pressing and 10 minutes before half-time midfielder Andrew Crofts was presented with a good opportunity 10 yards out, in a central position, but he sent his header over the top.
Stuart Parnaby started a league game for Boro for the first time since 2006, replacing Justin Hoyte who suffered a pulled hamstring at Watford two weeks ago, and he and his fellow defenders managed to keep Brighton at bay in the second half.
Poyet sent on attacking substitutes Stephen Dobbie and Will Buckley - and both players went close to levelling matters, before Boro keeper Steele pulled off a fine save to push away an Ashley Barnes effort from 25 yards.
The Seagulls did have other chances, particularly through Mackail-Smith, but they failed to score for the fifth Championship match in a row.