The former England international, who lost his maiden game at the helm at Mansfield last weekend, guided Carlisle to three much-needed points in his first home game in charge courtesy of David Amoo's 72nd-minute strike.
After a full week working with their new manager Carlisle's plight looks less ominous than before with only three points separating five teams at the bottom.
Of the sides around them only Hartlepool United were able to collect a point as the others, including Tranmere, all lost.
Second-bottom Oxford United slipped to a fifth league defeat of the season away to Luton Town, who had Luke Wilkinson and Jake Howells to thank for their 2-0 win.
Meanwhile, York City's slow start to the campaign continued as they were beaten 2-0 at Dagenham and Redbridge.
At the top, Burton Albion bounced back from two consecutive losses as Stuart Beavon's strike gave them a 1-0 win over Cheltenham Town.
Gary Rowett's men had lost top spot but Beavon's second goal of the campaign saw them replace Bury at the summit after the Gigg Lane outfit lost 2-1 at Exeter City.
Wycombe Wanderers climbed to second place, just a point behind Burton, after Paul Hayes' scrappy 63rd-minute goal secured a 1-0 win over a Cambridge United side who have now lost three on the bounce.
Southend United's fourth win in a row over 10-man Shrewsbury Town lifted them up to fourth, while Northampton Town's inconsistent campaign continued as they put last weekend's incredible 5-4 defeat to Accrington Stanley behind them to beat Morecambe 1-0.
Newport County and Stevenage both enjoyed three-goal winning margins, the Welsh outfit prevailing 4-1 against AFC Wimbledon, while Mansfield Town were beaten 3-0 at the Lamex Stadium
Elsewhere, Jon Coleman guided Accrington to a second successive win as they beat Plymouth Argyle 1-0.
