Italy trimmed the lead through two Bergamasco penalties, but Wilkinson's drop-goal soothed England nerves.
The French visitors got a late try from Italian international Mirco Bergamasco, but it was mere consolation.
Tight-head Euan Murray was penalised for standing up in the scrum and Bergamasco slotted over the simple penalty.
Julien Saubade crossed with 10 minutes left and Mirco Bergamasco's late 70m run-in gave Stade a bonus point.
The Italians took the early initiative and Mirco Bergamasco slotted two penalties before Dan Parks replied to square the scores at half-time.
But Canavosio found a gap to touch down under the posts and Bergamasco's conversion ensured an Italy victory that leaves Scotland without a point.
Italy claimed their solitary try as Mirco Bergmasco finished off a sweeping move after 72 minutes to cap a mixed day for the Bergamasco brothers.
But England could not take advantage of the Leicester tight-head's absence and Italy even managed to reduce the lead as Bergamasco landed his third penalty.
They came desperately close to scoring through Rougerie just before the hour mark, only for him to be denied by a superb Mirco Bergamasco tackle.
Ellis scored England's fourth try after the break and although Italy cut the gap through Mirco Bergamasco, Mark Cueto had the final word for the hosts.
That meant England led 22-6 at half-time and Italy finally accepted the inevitable, removing Mauro Bergamasco and bringing on Giulio Toniolatti for just his second cap.
Lachie Turner's score established an 8-3 lead for Australia but a drop goal and Mirco Bergamasco's try put the hosts in the driving seat at 14-11.
The Azzurri have been accused of illegal tactics in the contact area and flanker Mauro Bergamasco has been picked out as one of the main culprits.
Bergamasco is a fine open-side with 69 caps to his name but his inexperience at number nine cost his side a try within two minutes of the kick-off.
It then went from bad to worse for Bergamasco as his horrendous pass eluded Gonzalo Garcia and Goode kicked ahead before Flutey gathered the ball and went over.
Stade had the final say when wing Bergamasco went over in the right corner for his side's third try, Lionel Beauxis' conversion proving his side's only successful kick.
The hostile atmosphere took a turn for the worse when Paul Volley's elbow on Mauro Bergamasco led to a brawl involving most of the players on the pitch.
Parks penalties twice put the Scots ahead, with Bergamasco replying.
By now, Mirco Bergamasco had been handed the kicking duties for Italy and while he missed the conversion, he did notch a penalty five minutes into the second half.
Mirco Bergamasco sealed the bonus point for Stade by running in from long range after more turnover ball, while Barry grounded a consolation try for Quins in injury time.
Italy's kickers Mirco Bergamasco and replacement fly-half Luciano Orquera missed 10 kickable points between them and Italy, who conceded five penalties, spurned some kickable opportunities in the second half.
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However, Gonzalo Canale made an excellent break four minutes later before offloading to replacement scrum-half Canavosio, who touched down under the posts for a try that was converted by Bergamasco.
That score further fired up the Italians and they extended the lead four minutes later after a dubious offside decision gave Bergamasco another easy kick in front of the posts.
Italy also failed to take their first chance, Andrea Marcato missing a penalty for the visitors, and they shipped a second try after 18 minutes following a second Mauro Bergamasco error.
Stade grabbed the next try to take firm control of the match, with Malone coughing up possession before Jerome Fillol, Mauro Bergamasco and Skrela combined to give Dominici a simple score.
Italy looked to have genuine claims for an infringement when Bergamasco powered down the wing only to be shoulder-charged by Southwell, earning his 50th cap along with Chris Cusiter, after kicking ahead.
In contrast Italy boss Nick Mallett decided to gamble by picking the older of the Bergamasco brothers, Mauro, normally a flanker, at scrum-half because they had lost their three leading number nines to injury.
Italy won a penalty for offside two minutes after the break despite the ball being outside the ruck and Bergamasco launched the ball between the posts to put the home side back in front.
Italy once again lost control of the ball at the base after Bergamasco had been sucked into a ruck and Haskell's flick saw Ellis scamper 20m to the line and dive over for an unconverted try.
They cut the gap to just two points with 10 minutes remaining with a fourth penalty from Bergamasco and for a moment it looked as though they would reel England in to claim their first ever win over the visitors.
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