A fiercely contested first half saw Cardiff Blues fly out the traps and take an early 6-0 lead inside of 13 minutes courtesy of Rhys Patchell’s trusty boot.
However, the English side slowly worked their way back into the game and cut the lead to three points by the break after a penalty from Ben Botica.
Two tries in the space of two bad minutes for the home side saw Quins take control after the interval as an intercept from Tim Visser was quickly followed by a score from Ollie Lindsay-Hague.
A third visiting try from wing Charlie Walker looked to end the game as a contest until a home penalty try after a collapsed rolling maul sparked a fight-back.
Matthew Rees was red carded late in the game before Sam Hobbs crashed over from close range to ignite bonus point hope.
But it was Quins who took the maximum points on offer as a last minute try from England international Danny Care ensured they took the spoils and went top of the pool.
Harlequins were without a number of their injured stars while Cardiff Blues were forced into a late change as Wales skipper Sam Warburton was ruled out through illness.
A back row reshuffle saw Manoa Vosawai come in at Number Eight, Josh Tunbull switch to blindside flanker and Ellis Jenkins slot in an openside.
Both teams came into the European game unbeaten after opening round victories and jostling for the summit in Pool 3 in the early stages of the competition.
But it was the London outfit who took control of proceedings leaving Wilson’s men to face the December double-header against Montpellier to get their qualification hopes back on track.
The start of the game saw a superb minute’s applause in recognition of former Cardiff Blues player Jonah Lomu, who sadly passed away earlier in the week.
And the thunderous ovation continued at kick-off as the home forwards immediately drove up the middle then won a scrum penalty that was slotted to the corner. The driving lineout, though, was held out as the ball was knocked on close to the line.
Ellis Jenkins won a brilliant penalty with a superb turnover on the floor as Quins held on and Patchell slotted the opening points of the night on eight minutes.
Wing Alex Cuthbert drew cheers as he snagged Lindsay-Hague as he took a high ball as the hosts looked to play with real tempo and aggression early on.
All-action back row Jenkins again stripped ball on the floor to win possession and Blues came strong as Gavin Evans arched a run into space and prop Taufa’ao Filise went hard in contact as the ball was worked back in field.
The home side were dominating territory and were rewarded again as the inspired Jenkins hit the line at pace, Lloyd Williams edged closer with a stretch for the line and Patchell did the rest when the penalty was won.
Centre Rey Lee-Lo broke away before his neat inside offload only found early replacement Dave Ward who countered for the visitors down the wing.
Wing Tom James pinned Quins back with a sweet kick in behind, but the English side returned the ball with interest as the backs slung the ball around and the forwards powered into bodies.
The penalty eventually went the visitors way to reward the possession, but Botica saw his kick cannon back off the right post.
However, a scrum five-metres out, as Cardiff Blues were caught playing from deep, saw more sustained pressure before a stolen lineout from Kristian Dacey saw Patchell smash a clearing kick.
Back came the visitors from deep as England international Nick Easter broke tackles and Charlie Walker burst down the flank.
The ball was worked in field to skipper Jack Clifford, but the flanker took a heavy clash of heads and was stretchered off after a lengthy stoppage.
When the game restarted after several minutes, fly half Botica made up for his earlier miss with his first successful kick of the night.
Matt Hopper then cut a slicing run through as Quins battered the home line, but this time as the ball was worked right a combined effort from Lee-Lo and Evans saw them rock Harry Sloan back on his heels on the stroke of half-time.
Blues made a half-time change as Lou Reed replaced Jarrad Hoeata and the home side gained early territory when Botica kicked a ball dead as he went for a deep touch finder.
However, it was the Londoners who were playing all the rugby as they kept the ball in hand, trucked it up and after Ward’s break they deservedly levelled with Botica slotting the easy kick.
Three minutes later disaster struck for the hosts as a pass was picked off in a congested midfield by Visser who opened his legs and ran in from halfway, despite Patchell’s brave chase, to open up a 13-6 lead.
And within 60 seconds it went from bad to worse as the visitors scored again as quick hands opened up space and full back Lindsay-Hague tore away and showed all his pace to score under the posts and open up a 20-6 lead.
Cardiff Blues were dealt a further blow when the impressive Ellis Jenkins was stretchered off and replaced by Macauley Cook before the hour mark.
The home side looked for a way back into the game with Matthew Rees and Lou Reed both rumbling up close to the line.
But it was Quins who extended the leads 15 minutes from time when wing Charlie Walker was on the end some neat handling from Danny Care and Ward to wriggle his way over and touch down.
Cardiff Blues did hit back within five minutes as the home pack marched on and referee Alexander Ruiz awarded a penalty try as the rolling maul was pulled down, that replacement Jarrod Evans converted to cut the lead to 13-25.
Any hope of a fight-back looked short-lived when a red card to Rees ensured Blues would play the final seven minutes a man down.
However, a superb late effort saw Sam Hobbs touch down, after Fish’s quick break, and Evans slot the conversion to cut the lead to five points.
But in one final twist the home side lost the ball as they played from deep and it was Care who stripped possession and darted away to give Quins maximum points in Cardiff.
08m Patchell p 3-0
13m Patchell p 6-0
34m Botica p 6-3
47m Botica p 6-6
50m Visser t Botica c 6-13
52m Lindsay-Hague t Botica c 6-20
65m Walker t 6-25
70m Penalty t J Evans c 13-25
79m Hobbs t J Evans c 20-25
80m Care t Swiel c 20-32
Cardiff Blues: 15 Blaine Scully (Fish 51), 14 Alex Cuthbert, 13 Rey Lee-Lo, 12 Gavin Evans (J Evans 62), 11 Tom James, 10 Rhys Patchell (G Evans 63), 9 Lloyd Williams; 1 Gethin Jenkins (Hobbs 69), 2 Kristian Dacey (Rees 59), 3 Taufa’ao Filise (D Lewis 51 (Filise 62)), 4 Jarrad Hoeata (Reed 40), 5 James Down, 6 Josh Turnbull, 7 Ellis Jenkins (Cook 53), 8 Manoa Vosawai (Dacey 75)
Replacements: 16 Matthew Rees, 17 Sam Hobbs, 18 Dillon Lewis, 19 Lou Reed, 20 Macauley Cook, 21 Tavis Knoyle, 22 Jarrod Evans, 23 Dan Fish