Wales’ Capital Region went into the encounter on the back of consecutive victories over Zebre and the Ospreys and they made it three on the bounce to finish the regular season on a high.
The first-half tries gave the Blues a 14-11 lead at the interval but they were frustrated for large periods of the second half.
Gareth Anscombe kept the hosts at arms length, stretching his personal tally with the boot to 16-points to secure the victory.
It ensures Danny Wilson’s men finish seventh and they now travel to France to face the seventh-placed Top 14 team, unless Stade Francais win they European Challenge Cup.
Playing at the Constructaquote Stadium in Caerphilly, it took the hosts little more than one minute to claim the opening try.
Carl Meyer ran back a clearance to make the initial inroads and the Dragons remained in the ascent. They went through several phases before Angus O’Brien dinked a cross-kick to the right-hand corner where the full-back collected unopposed.
O’Brien missed the conversion but the Dragons continued to cause Cardiff Blues problems and the fly-half added a penalty on seven minutes to bring the scores to 8-0.
Following the penalty there was a touching minute’s applause in support of Dragons number eight Ed Jackson, who is currently in hospital after suffering a serious spinal injury.
However the Blues responded ten minutes later with Morgan grubbering through and collecting after Cuthbert hacked on.
The full-back finished spectacularly and Anscombe added the extras from the touchline before O’Brien knocked over a second penalty after Macauley Cook was penalised for a high tackle.
Kingsley Jones’ men remained in control, largely courtesy of a strong wind, but the Blues burst into life just before the half-hour mark.
Halaholo released Matthew Rees with a no-look pass and he surged forward before a sensational period of interplay between forwards and backs took the Blues into the Dragons’ twenty-two.
The ball was moved to Alex Cuthbert on the right and then back to the left where Halaholo cut inside and beat three defenders.
Anscombe again converted to give his side the lead for the first time and they continued to press in the closing stages but the score remained 14-11.
The fly-half booted the scoreboard back into action on 52-minutes and his side dominated both territory and possession in the third quarter.
The Dragons were dealt a blow when Thomas Rhys Thomas was sent to the sin-bin for a neck-roll and the Blues continued to hammer away.
However they were unable to breakthrough as mistakes frustrated and the Dragons clung on.
Following a sustained period of pressure, in which Cardiff Blues failed to find a scoring pass, Anscombe nailed his second penalty to stretch his side’s lead to nine-points.
Meyer quickly responded with a superb long-range penalty and he bisected the posts again on 72 minutes to set up a tense finale.
A pair of Anscombe penalties gave his side some breathing space going into the final five minutes, but a late try from Sam Beard set-up a nervy finale for Danny Wilson's side.
However, the home side couldn't secure a late winner, as Cardiff Blues go into the European play-off on a winning note.