However, it was scrum half Dan Robson who saved the day, as his charge down of Camille Lopez's attempted drop goal clinched the win.
It was a victory that was earned the hard way, and actually looked unlikely for much of the second half as Gloucester battled to peg back a fired up home side.
To be fair, it was largely Gloucester errors that had given the home team so much hope and a foothold in the game.
Missed tackles led to the two Bordeaux tries in the first half. With Lachie Munro keeping the scoreboard ticking over, it was a night that could have gone badly wrong.
But, time and again this season, Nigel Davies' side have looked down the barrel of a defeat yet emerged with a win.
They did so with two penalties in the last five minutes, which turned a potentially losing 26-25 scoreline into a winning position.
It wasn't pretty, and Gloucester will have much better days at the office. However, pool one is now secure and, a win next weekend against Mont de Marsan, will clinch a home quarter final.
It was a damp, cool evening at the Stade Andre Moga, and Gloucester's preparations were disrupted when they were caught in bad traffic on their way to the ground.
The home side made the brighter start as a crucial tackle was missed in midfield allowing flanker Kitshooff to gallop downfield. The defence recovered, but at the expense of a penalty. Lachie Munro opened the scoring easily.
Freddie Burns was given an immediate chance to reply in kind as Gloucester won valuable turnover possession, and the new addition to England's senior squad made no mistake.
It was lively stuff from the home side in the opening exchanges. They were backed by a small but vocal crowd, and were asking questions early of the Gloucester defence.
Nigel Davies' side were struggling to get their hands on the ball, and having to work hard without it. It came as no real surprise when Munro added a second penalty on 14 minutes for a 6-3 lead.
The sluggish start continued and it was bad news for Gloucester. The Gloucester midfield fell off a tackle on centre Charles Brousse, and he put Raphael Carballo into the corner. Munro converted for 13-3.
Alarm bells were gently ringing for Gloucester, but some powerful ball carrying from Qera and Morgan got them on the front foot and Burns was able to add a second penalty of the evening.
More good breakdown work followed immediately, Morgan hacked downfield and the ensuing panic in the home defence resulted in a third penalty for Burns on 25 minutes.
It had been a tough half hour for Gloucester, but the pack then took things into their own hands.
A well executed catch and drive from ten metres out produced a try for Darren Dawidiuk and Freddie Burns converted for a 16-13 Gloucester lead.
Led by Jim Hamilton, the forwards seemed to have found their groove. The Scotland international leapt to nick a home lineout on 37 minutes, and a fourth penalty for Burns followed.
The tide looked to have turned but, unfortunately for Gloucester, there was one last sting in the tail in the first half.
Good offloading work from the home forwards set up superb field position in the Gloucester 22 in front of the posts.
Centre Brousse broke another tackle, and prop Tamato Leopolu burrowed over from close range. Munro's conversion nudged his team back in front, 20-19, at half time.
It had been a real Jekyll and Hyde performance from Gloucester. They had started sluggishly, perhaps due to their delayed arrival.
However, they rolled up their sleeves and battled their way back into the game, scoring 16 unanswered points, only to surrender the lead with the last play of the half.
A try just before half time last weekend had proved pivotal to the overall outcome. Hopefully, lightning wouldn't strike twice.
The half time team talk from Director of Rugby Nigel Davies was going to be a key one but Gloucester would know that this one was more than winnable, if they could just cut out the errors.
The second half started with Gloucester on the front foot, but a knock on turned a promising attacking position into one of real danger as Bordeaux hacked downfield.
Gloucester got back through Burns but killed the ball near their own line, and Lachie Munro, who had looked secure in his goal kicking all night, bisected the posts for 23-19.
There was then another real let off as a quick tap caught Gloucester napping, but Nick Wood saved the day as he snaffled an offload near his own line.
Burns and Munro swapped penalties to maintain the four point gap, before Gloucester were dealt a real blow when Huia Edmonds was sinbinned having only been on the pitch for a minute.
Shaun Knight took over the lineout throwing, and made a good fist of things. A 63rd minute Burns penalty made it 26-25 and the tension grew.
Tim Molenaar very nearly made two crucial breaks, but couldn't quite get away and it was left to the trusty right boot of Burns to edge Gloucester back in front with his seventh penalty of the night.
Bordeaux-Begles still couldn't quite be shaken off. A dubious high tackle was given against Will James, and the home side kicked deep into the Gloucester 22.
The French side patiently worked their way into drop goal range, and fly half Lopez set himself for the go ahead drop goal.
He reckoned without the speed of Dan Robson, who reached 32 kph according to the team analysts, charged him down and then followed up as Dan Murphy hacked downfield, dragging the covering Bordeaux player over his own line.
Gloucester won a penalty at the 5 metre scrum, and Burns' eighth penalty of the night sent the travelling supporters into ecstasy.