The striker who was making his first start of the season, scored a hat-trick in a throwing 16-minute spell in the second half. It enabled City to stage a stirring recovery after they had fallen behind to a goal from Andy Keogh which had left the home fans stunned.
And at that time the fans must have been casting their minds back to earlier in the season when they lost at Doncaster, another League One club, in the Carling cup.
And with their record against lower league opposition unconvincing - previously they had lost at Shrewsbury, Halifax, Blackpool and Oldham - there was a sense of foreboding when Keogh struck for Scunthorpe.
City fielded a new look strikeforce as Fowler was given a rare appearance alongside Antoine Sibierski as Andrew Cole and Darius Vassell were taken out of the front line.
Stephen Jordan came in for Ben Thatcher at left-back as manager Stuart Pearce made three changes from the side beaten at home by Tottenham three days earlier.
Scunthorpe made a confident start and early on Ian Baraclough curled a free-kick narrowly wide. Fowler almost made his mark after being put through by Joey Barton only to fire agonisingly wide.
City was stunned however when Scunthorpe stole into a 17th minute lead when Keogh sprang the City offside trap running on to a throughball from Cliff Byrne before slotting a shot low past goalkeeper David James.
Scunthorpe defended resolutely and restricted City to hardly any first-half chances and the visitors might even have added a second goal when after a quickly taken free-kick Keogh set up striker partner Billy Sharp, whose goalbound shot was deflected by Richard Dunne for a corner.
Pearce made a half-time sub bringing on Lee Croft for Nedum Onuoha and switching Sun Jihai into defence. The introduction of lively winger Croft immediately transformed the fortunes of City as within three minutes he had set up the equalising goal for Fowler.
Croft burst down the left and fired over a low cross which Fowler fired high into the roof of the net from six yards, his first senior goal since April.
The revitalised Fowler struck again in the 56th minute when Stephen Ireland crossed from the right and the former Liverpool, Leeds and England striker found the net with a low shot which went in off the upright.
Fowler completed his treble and earned the right to keep the match ball midway through the half with a penalty which he coolly slotted home following a handball from Scunthorpe defender Michael Rose.
It was a remarkable turnabout because at the break City were behind and were devoid of ideas and looked as though they could easily crash out of the cup.
But at the end they might have won by a wider margin as Scunthorpe's spirits drained visibly. Trevor Sinclair, Bradley Wright-Phillips and Dunne all had clear-cut chances as City's confidence soared in the second half.
Man City man of the match: Robbie Fowler - The former Liverpool ace made a stunning return to the City ranks with a hat-trick that ended the visitors' hopes of an upset.
Scunthorpe man of the match: Ian Baraclough - Offered a strong presence in the Iron midfield and was accurate with his deliveries from set-pieces for the League One battlers.