The centre spent the last two weeks on the side-lines but returned to the starting line-up to impressive effect.
It was his break that made the inroads for Blaine Scully’s try and following the break he twice eased past the Pau defence to touchdown.
The victory ensured Danny Wilson’s men leapfrogged Bath back to the top of Pool Four ahead of their December double header.
A minute’s silence was observed impeccably by the BT Sport Cardiff Arms Park crowd who honoured the 144 victims of the Aberfan disaster and paid tribute to Anthony Foley.
Fifty years to the day the tragic accident hit Pantglas Junior School in the mining village, while Munster coach, and former player, Foley passed away last week.
The Blues opened the scoring inside three minutes with Steve Shingler providing the flat pass and Allen the razor sharp line to cut the Pau defence in half.
Allen found Dan Fish on his outside who delayed his pass to perfection to give Scully just enough space to finish in the corner.
Shingler converted expertly from the touchline and he knocked over a straightforward penalty on 10 minutes to open up a 10-0 lead,
Pau crossed from their first real period of pressure with Daniel Ramsey charging over from close-range but they failed to add the extras and Shingler kept the scoreboard ticking for the hosts.
They were unable to build further on their advantage with the French visitors enjoying plenty of territory and possession.
The Blues held out a sustained attack in the closing stages of the half, hitting the gigantic Pau pack with equal venom as the scores remained 13-5 at the interval.
Wales’ Capital Region started the second-half well and Garyn Smith and Allen combined beautifully in the centre to almost claim a second try.
Allen was caught and possession was maintained with Alex Cuthbert making good yards. Pau were penalised and the ball was dinked to the corner only for a miscommunication.
No Blues jumper went up but Pau slapped the ball over their own dead ball line to concede a five metre scrum.
It held steady and from a set move, Shingler floated a miss-pass for Allen to ease around his opposite number to score under the sticks.
The fly-half added the extras to make it 20-5 after 50 minutes and the Blues remained in the ascendant.
Macauley Cook rampaged through a ruck before galloping 30 metres, the ball was recycled and Allen threaded a neat grubber to the corner with Scully beaten by only the touchline.
But ten minutes after his first, Allen completed his brace again from a set-play from a scrum, ghosting around the defence following a fine Shingler flat-pass.
Shingler was once again on target to stretch the Blues’ lead to 27-5.
Pau dotted down for a late consolation try, through Bastien Pourailly, but the 27-12 final score ensured Cardiff Blues kept their 100 per cent record in the European Challenge Cup this season.