Selby came on strong in the final round to edge out his great rival Conlan and retain the title he first won in Moscow two years ago.
The 24-year-old Welshman has now won four consecutive European medals having also picked up bronze medals in 2008 and 2010.
The result meant more heartbreak for Belfast man Conlan, who was pipped by Selby in their World Championship quarter-final in 2011, and also lost a superb battle in this year's World Series of Boxing.
But there was double joy for Ireland as both Olympic silver medallist John Joe Nevin and middleweight Jason Quigley were crowned champions.
Nevin outclassed Ukrainian southpaw Mykola Butsenko to claim a unanimous points verdict, while Quigley edged out Romania's Bogdan Juratoni via a split decision after a thriller.
Ireland's Paddy Barnes was forced to settle for a silver medal after withdrawing from his scheduled light-flyweight final against Russia's David Ayrapetyan due to a nose injury.
Leeds light-flyweight Jack Bateson and London super-heavyweight Joe Joyce were awarded their bronze medals after bowing out at the semi-final stage on Friday.