The 44-year-old Fenlon resigned on Friday afternoon claiming he had taken the club as far as he could.
But caretaker boss Jimmy Nicholl could not inspire the Easter Road side to better luck as former Celtic skipper McManus' goal 23 minutes in sealed a 1-0 triumph for Well, who ended the match a man down after Shaun Hutchinson's late red card in a game which was screened live on BT Sport.
Fenlon's former number two only found out he was taking over the reins less than 48 hours before the Scottish Premiership fixture.
Irishman Fenlon claimed Wednesday's 1-0 Scottish League Cup quarter-final loss to financially-stricken city rivals Hearts was not the reason for his departure, but the nature of the derby defeat only laid bare his struggles when it came to motivating the Leith outfit.
However, in spite of two embarrassing reverses to their Edinburgh foes and the 9-0 aggregate Europa League disaster against Malmo, the team he leaves behind are not a total lost cause and they arrived at Fir Park knowing victory would take them to joint-fifth alongside St Johnstone and just one point behind Sunday's Lanarkshire hosts.
Inverness manager Terry Butcher now appears to be the favourite to replace Fenlon but Hibs' toothless showing against Stuart McCall's men - another defeat after losing to Aberdeen and Hearts in recent days - proves that whoever gets the job will have to work strenuously to cajole consistent results from a side bereft of confidence.
Motherwell, meanwhile, themselves kicked off feeling the effects of a hangover after their own cup exit at the hands of Aberdeen in midweek and the muted atmosphere round their home ground only reflected the sullen mood of both sides.
Hibs striker Paul Heffernan wasted two decent chances to lift his team within the opening 10 minutes, though, as he first put wide from Kevin Thomson's front-post cross before shooting wildly past Gunnar Neilsen's frame after Liam Craig had put him through on goal.
The Dubliner sent another opportunity into the Well keeper's hands after Tom Taiwo picked him out in the box but he was soon regretting his wastefulness as the Steelmen found the net.
Lionel Ainsworth sent a corner towards the near post which McManus got to first ahead of Ryan McGivern before powering a header past Leith keeper Ben Williams.
A second should have been struck just after the half-hour mark as John Sutton released Henri Anier for the Estonian to shoot between the Hibs number one's legs.
However, the ball clipped the inside of William's heel and ricocheted wide of the target for a save he knew nothing about.
Hibs thought they had a leveller as Scott Robertson jinked past three men on his way into the box but Fraser Kerr - an early replacement for the injured Simon Ramsden - came up with an important last-ditch block.
At the other end, Williams saved again from Anier after the striker wriggled past Jordon Forster before Stuart Carswell poked wide.
Nicholl made his first change on 64 minutes as he replaced Taiwo with Abdellah Zoubir, and the tricky Frenchman immediately added a new dimension to the wavering visitors. His first act was to set up Craig to shoot from 25 yards out, although Neilsen did well to parry the strike away.
Hutchinson's last-man trip on Heffernan saw his afternoon end three minutes early as referee Crawford Allan showed him a straight red, but Rowan Vine wasted the free-kick that followed as he rammed it straight into the wall.
Hibs still had chances to grab a point in stoppage time but substitute James Collins first fired wide before Heffernan was denied by Neilsen's outstanding diving save as Motherwell grabbed the win that sees them move into joint-second alongside Inverness.
- Sports & Recreation
- Jimmy Nicholl
- Shaun Hutchinson
- Paul Heffernan