Jamie Murphy and Steven Saunders both headed home inswinging Stevie Hammell deliveries midway through the first half to earn Stuart McCall his first Scottish Premier League win as Motherwell manager.
Zemmama blazed over from the spot a minute before half-time, and Hibs failed to seriously test Darren Randolph despite enjoying the territorial advantage in the second period.
With half of Hibernian's four wins this season coming against Motherwell, they may have welcomed the trip to Fir Park following their midweek Scottish Cup exit against Ayr.
But the concession of soft goals and their inability to make possession count suggest they are in for a relegation battle after falling to second bottom of the SPL.
Hibernian have not won in 10 games or scored for five as manager Colin Calderwood struggles to find his best team. Calderwood dropped Derek Riordan as he made four changes to the team that lost at Somerset Park.
Callum Booth made his first Hibernian start at left-back with Steven Thicot coming in at right-back. Paul Hanlon moved to centre-back, allowing Ian Murray to join the recalled Danny Galbraith and Merouane Zemmama in midfield.
McCall handed Northern Ireland international Steve Jones a debut on the left flank following his loan signing from Walsall. The Motherwell boss had been hoping to field striker Mike Grella after taking him up from Leeds but the Scottish Football Association blocked the loan transfer after refusing to recognise his spell at Carlisle as an emergency loan.
Despite the comfortable win, and a fourth clean sheet in five games, McCall is still in need of reinforcements after Motherwell finished the match with most of their team aged 21 or under and struggled to create chances in the second half.
The home side took less than 60 seconds to threaten though when Murphy flicked on Saunders' long throw but Graeme Smith smothered as John Sutton followed in.
Hibs settled but had nothing to show for their possession and Motherwell notched their first SPL goal of 2011 in the 20th minute.
The Hibs defence stood still as Hammell swung in a free-kick and Murphy glanced a header which bounced over the hand of the diving Smith.
The former Motherwell goalkeeper, making only his second SPL appearance since conceding six goals in the thrilling Fir Park draw in May, was beaten at his near post in the 24th minute when Saunders met Hammell's corner.
Motherwell continued to create half-chances - Sutton was unable to turn another inswinging corner from Hammell on target under pressure and Smith held Murphy's long-range drive.
Hibs got a lifeline when Saunders handled inside the box as he and Shaun Hutchinson collided while trying to clear Galbraith's cross. Zemmama had released Galbraith with a clever pass but he lost his composure from the spot as he swept the ball high over the bar.
Hibs were unhappy that referee Alan Muir had blown for the penalty while Rankin prepared to take down Galbraith's cross at the far post.
And their frustration continued after the break when assistant manager Derek Adams, who is in the process of appealing against a lengthy touchline ban, was sent to the stand on the advice of fourth official Kevin Clancy.
The home side allowed Zemmama another chance thanks to sloppy marking at a throw-in but Darren Randolph held his volley.
Nish had replaced Darryl Duffy at half-time and his aerial presence created a half chance following Zemmama's cross, but Galbraith leant back and shot well over.
Zemmama curled a free-kick a yard over as Motherwell struggled to settle in the second period, not helped by the loss of Tom Hateley to injury.
Steven Meechan came on and Jonathan Page soon joined him in midfield to shadow Zemmama after replacing Jones, who had shown some neat touches.
Riordan came on for Rankin and Hibs continued to press but they could not cut Motherwell open. Randolph comfortably held two Riordan free-kicks and Nish volleyed over from a tight angle as Hibs drifted to another defeat.