Tranmere were reduced to 10 men after 35 minutes when Jean-Louis Akpa Akpro was sent off for kicking out at Frank Simek.
Loy made the most of Carlisle's one-man advantage just before the break when he connected with Matt Robinson's cross.
Bournemouth closed the gap on Tranmere and second-placed Doncaster as they recorded a 3-0 win over 10-man MK Dons.
Lewis Grabban opened the scoring before Ryan Lowe was sent off just before the break.
Marc Pugh still had time to score the Cherries' second before the half-time whistle, with Harry Arter adding the third in the 84th minute.
Bury beat Doncaster 2-0 thanks to goals by Andy Bishop and Nick Ajose.
Bottom side Hartlepool were victorious against Notts County and secured only their second home win of the season with a 2-1 victory.
Hartlepool went ahead when James Poole scored from close range before County equalised through Jamal Campbell-Ryce.
Peter Hartley had the final word, though, when he nodded in Evan Horwood's free-kick.
Yeovil claimed their fifth successive league win with a 3-0 victory over Brentford.
Paddy Madden scored his 14th league goal of the season and Ed Upson hit a spectacular second before Dan Burn volleyed a late third to seal victory.
Colchester saw off the late challenge of Portsmouth to win 3-2 after they scored three early goals at Fratton Park.
Gavin Massey scored either side of Jed Wallace's goal for Pompey, with Freddie Sears firing in a penalty for Colchester in the first 20 minutes.
James Keane scored for Portsmouth after the break but the scoreline remained at 3-2 in the visitors' favour.
Elsewhere, Shrewsbury came from behind to beat Preston 2-1 at Deepdale.
Stuart Beavon put the home side ahead just before the break, but a goal by Jon Taylor and penalty by Matthew Richards saw Shrewsbury take the points.
Walsall also came from a goal down to beat Oldham 3-1 at the Banks's Stadium.
Debutant Lee Barnard headed Oldham into the lead in the 19th minute before James Baxendale levelled with five minutes of the first half remaining.
Jamie Paterson fired home a brilliant goal from outside the area in the 75th minute before he made sure of the win in stoppage time with another strike.
Elsewhere, Ajay Leitch-Smith's goal was enough for Crewe as they beat Scunthorpe 1-0 while Leyton Orient were 1-0 winners at Stevenage thanks to Dean Cox's 10th minute effort from inside the six-yard box.
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