Welsh international centre Allen slid over for a first half try and the boot of man-of-the-match Gareth Anscombe – with a penalty and drop goal – ensured that Blues ultimately made the shirt trip back west with four points.
But that was only half the story in a heart-stopping finale as Blues were forced to dig deep to hold on and avoid Dragons doing the league double.
An ambitious late drop goal attempt from halfway clipped a visiting hand to give Dragons a five-metre with only a matter of seconds left.
However, the Blues pack held firm and a penalty was awarded to Mark Hammett’s men to signal the start of derby day celebrations and the perfect way to kick off the new calendar year.
Dragons had won the corresponding fixture at BT Sport Cardiff Arms Park just a week ago and looked to pick up where they left off with a fast start.
Former Blues player and home scrum half Richie Rees snapped up a wayward first visiting lineout and the returning home hero Taulupe Faletau took ball on before a penalty for offside gave Tom Prydie a simple kick to put Dragons ahead.
In response, a high hanging kick from Anscombe caused alarm, as Faletau fumbled and then Prydie repeated the feat to give Blues an attacking platform. But the scrum penalty went against Hammett’s men and the promising early position was lost.
Blues did force a scrum penalty of their own, as the home front row popped up, to hand recalled fly half Anscombe a first sight of goal. But his effort was pulled across the posts and ended wide of the target on 11 minutes.
A clearing box kick from Tavis Knoyle flew out on the full, to hand Dragons another attacking position deep in the Blues half. But the scrum half made amends seconds later as Blues nicked the lineout and he this time drilled a superb low kick into the home 22.
Josh Turnbull and Josh Navidi punched holes with barreling runs before patient play from the visitors opened up space on 16 minutes in clinical fashion.
A flat pass from Anscombe took two men out of the Dragons defensive line and allowed Allen to arch a run towards the whitewash and use Lucas Amorosino as a dummy outside him, on the 17th
attacking phase, to step back inside and slide over for a 5-3 lead.
Gethin Jenkins was next to break clear, after another Dragons player shot out of the line hunting an intercept, and the prop quickly fed the supporting Anscombe on his right shoulder to make 30-metres up field before Hallam Amos dragged him down.
Another high up and under from Joaquin Tuculet was contested by Blues to win a scrum at the mid-point of the half. But another free kick against the visitors at the set piece halted momentum.
The game was rattling along at pace, as both teams traded kicks hunting territory, but with errors creeping in the fixture was being played out primarily in the middle of the park.
Allen was certainly looking lively with ball in hand while Tuculet was an elusive runner from deep.
And the forwards were putting in a huge shift with the back row trio of Turnbull, Warburton and Navidi all prominent ball carriers.
A penalty gave Anscombe a chance to kick to the corner and set up another visiting attack in the final ten minutes. However, a penalty against Taufa’ao Filise at the scrum, after the home side had nullified the lineout drive, allowed Dragons to clear and avert any danger.
The set piece was fast becoming a lottery as referee Ian Davies repeatedly penalised both sides and only one scrum out of 13 was successful as the half ended with Blues holding a narrow two-point advantage.
Blues made a half-time change, as Adam Jones replaced Filise as Blues looked to gain some control at the scrum, as it was the visitors who started the brighter this half.
Knoyle drilled a clever kick over Prydie’s head, Richard Smith cut a sublime line before Warburton smashed open a gap and Anscombe dropped into the pocket to coolly slot the drop goal.
Warburton was busy as he disrupted the breakdown before replacement Jones crunched his man into touch as the atmosphere and decibels cranked up another notch.
A penalty for dissent against Filo Paulo, as tempers boiled over, gave Prydie the chance to eat into the lead with a well struck penalty from wide right.
And another penalty, for not releasing against Allen, saw Dragons this time kick to the corner as they looked to build pressure. A quick tap and go by scrum half Jonathan Evans saw him look to feed Matthew Pewtner, but the wing lost control as he was shunted back.
Dragons were suddenly enjoying their best spell of the game as Tyler Morgan looked to exploit a gap and Faletau bashed through men before a penalty - for crossing - saw a home try ruled off.
Anscombe looked to respond as he broke the line before Allen and Knoyle looked to insert real pace. The forwards looked to drive on around the fringes, but just as Blues looked to making headway the ball was stripped and Dragons broke from deep.
A needless penalty for not rolling away gave Prydie yet another kickable penalty. However, he let Blues off the hook as his kick was wide right of the target. It would later prove crucial.
Back came Blues as the strong running Gavin Evans broke down the middle and tore Dragons wide open. Tuculet and Vosawai duly took ball forward before the visitors went right but Smith was held up by the weight of numbers.
Blues, though, had a resulting scrum five to attack from and immediately won the penalty. Anscombe needed no second invitation as he took the ball, pointed to the posts and drilled the kick over.
The game was swinging from end to end with Anscombe spotting a gap to break clear as Blues again looked to strike a decisive blow, only for Dragons to hold firm and win a penalty as Hobbs was isolated.
Late drama saw Tuculet spill a high ball and when Dragons hacked clear it was Amorosino who reacted first to race back and dot down for a 22 drop out, despite appeals from the home crowd that he had taken the ball over.
One last twist saw a long range drop goal from Dragons touched in flight by Amorosino to dramatically give the hosts a scrum five metres out with seconds remaining. But, as the home side pushed, referee Davies spotted an infringement and awarded Blues the penalty and win.
03m Prydie p 3-0
16m Allen 3-5
42m Anscombe dg 3-8
48m Prydie p 6-8
57m Prydie p 9-8
69m Anscombe p 9-11
Cardiff Blues: 15 Joaquin Tuculet, 14 Richard Smith, 13 Cory Allen, 12 Gavin Evans, 11 Lucas Amorosino, 10 Gareth Anscombe, 9 Tavis Knoyle, 1 Gethin Jenkins (Hobbs 71), 2 Kristian Dacey (Rees 56), 3 Taufa’ao Filise (A Jones 40), 4 Jarrad Hoeata (Cook 55), 5 Filo Paulo, 6 Josh Turnbull (Vosawai 55), 7 Sam Warburton, 8 Josh Navidi
Replacements: 16 Matthew Rees, 17 Sam Hobbs, 18 Adam Jones, 19 Macauley Cook, 20 Manoa Vosawai, 21 Lewis Jones, 22 Gareth Davies, 23 Adam Thomas