Bristol pulled one back on the stroke of half time to make it 2 - 1 at the break.
Thorne scored his second and City's third and despite Bristol pulling one back it was Cardiff's victory.
City now have played 2 and won 2 so far this season.
Report from Paul Evans.
It was great to to be able to escape the doom and gloom for a while this afternoon and watch a Cardiff City team win a game!
The youngsters didn't just win the game, I am not exagerating when I say that their first half performance was the best I have seen from a City team this season!
I have been moaning for a while now about the slow starts City make in home matches, but it's the complete opposite with the reserves. After scoring in the first fifteen seconds against Plymouth a fortnight ago, they took 22 seconds to find the net today, added another one two minutes later and then hit the post five minutes after that!
Peter Thorne was back today and it was one of his trademark clever headers that set Stuart Fleetwood free in the opening seconds, Fleetwood raced into the box, turned the wurzels right back inside out and then delivered a low cross which was knocked in from about ten yards at the far post by Tariq Khalil. Shortly after that Fleetood's clever pass set Thorne free inside the box and he easilly beat the keeper from about 12 yards and it seemed to be Thorne who hit the post later on with the wurzels defence at sixes and sevens following a free kick.
An action packed first few minutes ended with the unlucky Tariq Khalil picking up another injury and being replaced by Danny Thomas.
After the frantic start, the rest of the first half settled down into an open and entertaining affair with the wurzels having much of the play, but City's slick and clever passing ensured that they always carried the greater goal threat. Visiting keeper Clint Davies had to make good saves from a Michael Parkins free kick and a drive from the edge of the box by Danny Thomas, while Thorne wasn't far away with an angled effort.
City only had Thorne and Fleetwood with any league experience in their team, whereas Bristol had Fortune, Amankwaah and Woodman who had played plenty of matches for their first team. Added to that, they had a front two of Paul Heffernan their £100,000+ close season signing from Notts County and Steve Gillespie on a season long loan from Liverpool - for most of the first half, Anthony and Cronin at centreback for City coped well with these players, but, just before the break, a slip by Cronin let Gillespie in and, although Arran Lee Barrett made an excellent save to deny him, the ball then broke off a post for Heffernan to force in.
2-1 up at half time, the second half became an exercise in trying to hold on to what they had for City as the wurzels, with the wind behind them, got on top. However, the decisive moment of the game arrived after about 55 minutes when the diminutive Thomas, showing great strength to burst through a couple of tackles, set up a close range goal for Thorne.
City barely threatened after that as the more experienced visitors continuously pushed forward and they got a goal back with about twenty five minutes to go when Heffernan scored after some sloppy defending.
Gillespie really should have equalised with a close range header, Lee-Barratt produeced a fine save to flick a long range effort over the bar and, in the dying seconds, Skuse's shot cleared the bar by inches, but City held on to register another win at this level.
I would guess the wurzels will feel hard done by that they didn't get anything from the game and, I suppose, on the balance of play, a draw would have been the right result, but it has to be said that the City offered further proof that Paul Wilkinson has done a tremendous job with these youngsters.
To mention a few names, last year I had doubts about whether Arran Lee-Barrett had much of a future with us, but at the back end of last season and so far this year, he is proving me wrong! Byron Anthony was lucky to escape without a yellow card for a bad tackle on Heffernan, but, apart from that, he again showed why he has earned a professional contract, Joe Ledley showed his adaptability by playing in central midfield after Khalil went off. Michael Parkins showed some clever touches and Stuart Fleetwood caused the Bristol defenders all sorts of trouble in the first half.
One last thing, we don't beat the wurzels very often, so when we do, they are occasions to be savoured! Forget Swansea, this lot will always be our proper rivals to City fans of a certain age!