The Celtic nations are seen as being in direct competition for Group D's play-off spot behind world champions Germany and leaders Poland, with Martin O'Neill's side three points above Gordon Strachan's men ahead of the clash between the two former Celtic managers at Parkhead.
A scrappy first half was more notable for fouls and a fierce atmosphere in a stadium hosting a Scotland match for the first time since September 2006.
But Scotland grew in stature as the second period went on and snatched the points courtesy of Maloney's curled effort from 20 yards after a neat corner routine.
The win moves Scotland above Ireland into third place in the group with Gibraltar to come next in March.
Ireland, on the other hand, face a tricky test against Poland in Dublin and will now target next June's return fixture as a crucial encounter in their campaign.
Eyebrows were raised pre-match as O'Neill preferred Shane Long to record goalscorer Robbie Keane up front.
Aiden McGeady started on the wing and, as expected, the Scotland-born man received a frosty welcome from the home fans.
Hull City's Andy Robertson returned to Scotland's XI in one of three changes from their 2-2 draw in Poland last month and was quickly in the thick of the action.
Robertson's teasing cross was nodded behind for a corner from which Steven Fletcher thundered a header over the crossbar and the left-back's next teasing delivery then forced John O'Shea to deny Maloney a tap-in.
Grant Hanley went into the book for felling Long as he burst goalwards - referee Milorad Mazic not deeming the Blackburn Rovers man to be denying a goalscoring opportunity - and McGeady received a yellow card for a lunge on Fletcher to a predictably furious reception.
The testy nature continued as both sets of fans continued to make a din and Hanley may have been fortunate not to see a second yellow when he challenged David Forde with his arms raised, catching the goalkeeper in the jaw.
Charlie Mulgrew's fierce header under pressure from Seamus Coleman went wide and Fletcher made no contact when trying to flick the ball home - both chances set-up by Maloney as Scotland shaded the closing stages of a breathless half.
The second period began in a much more controlled manner, though Marshall had to be alert to tip McGeady's cross-shot away and substitute Chris Martin turned Steven Naismith's centre wide from six yards out at the other end.
That chance prompted a change of momentum in Scotland's favour and they grabbed the decisive goal with 15 minutes to play.
Maloney, who took the corner, played one-twos with Ikechi Anya and Scott Brown before curling a superb effort beyond the desperate reach of Forde.
Hanley almost headed into his own net in stoppage time, but was relieved to see his effort hit the crossbar and go behind as the hosts held on doggedly to consign Ireland to their first defeat in the group.
