The Latics took the lead a minute before half-time through captain Jason de Vos and extended their advantage with 16 minutes to go through an Andy Liddell penalty.
Joe Keith did reply in the last minute for the away side with a spot-kick of his own but Paul Jewell's men made it 11 wins in a row in the league, as they cruise towards promotion.
Oldham Athletic lost ground on the league leaders after coming from a goal down to earn a 2-2 draw at Wycombe Wanderers.
Wayne Andrews had given the visitors a 1-0 half-time lead but two minutes after the break, The Latics' Julian Baudet was sent off for abusive language and the extra man seem to change the course of the match for The Chairboys.
Richard Harris then equalised for the home side and Steve Brown looked to have threatened Oldham's unbeaten away record with a goal from the penalty spot with seven minutes to go.
However, Tony Carss snatched an equaliser a minute later for Iain Dowie's side, as both sides had to settle for a share of the points.
Crewe Alexandra moved to within a point of Oldham with a last-gasp 1-0 victory over bottom club Huddersfield Town at Gresty Road.
The match seemed destined for a scoreless draw, even with The Terriers down to ten men, after goalkeeper Scott Bevan was sent off for a deliberate handball just after the hour mark.
But Dario Gradi's side stuck to their task and Jones pounced to score the winner in the final stages to put behind Crewe's mid-week disappointment of going out of the FA Cup to Division Three side Bournemouth.
Cardiff City are level on points with Crewe after putting their disappointment of going out of the FA Cup to Coventry City behind them with a 2-1 home win against managerless Cheltenham Town.
The Bluebirds took the lead early through Peter Thorne but The Robins soon equalised through John Finnigan 11 minutes later.
However, Robert Earnshaw added to his goal tally by scoring the eventual winner for Lennie Lawrence's side nine minutes before half-time.
Bristol City's winless streak was extended to four matches after they were held to a 1-1 draw at resurgent Tranmere Rovers.
Mickey Bell had put the visitors in front after ten minutes but Simon Haworth equalised just after the hour mark to give both sides a share of the points.
QPR stay in the play-off positions following a good 1-0 away victory at Plymouth Argyle.
In-form Richard Pacquette scored the only goal of the match six minutes after the break at Home Park.
Ian Holloway's men finished the match with ten men after Lee Cook was sent off violent conduct in the last minute but QPR held on for all three points.
Luton Town moved up a place to seventh after an entertaining 3-2 victory at struggling Barnsley.
The Tykes had taken the lead in the first minute through Kevin Betsy and looked in even better shape when Luton goalkeeper Carl Emberson was sent for a deliberate handball nine minutes before half-time.
However, a man short, The Hatters were an inspired side as Matthew Spring equalised on the stroke of half-time before a brace from Tony Thorpe in the second half put Luton 3-1 up.
Bruce Dyer then made it interesting after scoring a penalty for Barnsley with 14 minutes remaining but Joe Kinnear's men held on to take the points in the end.
Chesterfield's hopes of putting themselves back in contention for a play-off position were hindered by a last-gasp 2-1 defeat against Mansfield Town at Saltergate.
Marcus Ebdon fired the home side ahead on 39 minutes from the penalty spot, after Matthew Gadsby's handled in the penalty area.
However just four minutes later, the visitors were level when Craig Disley's speculative shot found its way past Ben Williams.
Just when it looked like Stags player-manager Keith Curle would settle for the point, his side secured all three when Liam Lawrence netted for the visitors with virtually the last kick of the game.
Brentford had to come from behind to earn a 1-1 draw against struggling Notts County at Griffin Park.
Nick Fenton had put The Magpies in front on the stroke of half-time but Rowan Vine equalised six minutes after the break for the home side, as both sides shared a point.
Blackpool snatched a late winner to beat Northampton Town 2-1 at Bloomfield Road.
New Cobblers boss Terry Fenwick saw his side take the lead through Darryn Stamp in the first half.
However, The Seasiders equalised with 13 minutes to go with a penalty from Richard Walker and in the last minute, John Murphy snatched all three points with a second goal for Steve McMahon's side.
Swindon Town won a thrilling goal-fest of a match at Edgeley Park after beating Stockport County 5-2.
The Robins got goals from Sam Parkin, Steve Robinson, Alan Reeves, Matthew Hewlett and Eric Sabin to take the points.
Aaron Lescott and Richard Lambert scored consolation goals for player-manager Carlton Palmer's side.
Port Vale moved away from the Division Two drop zone with a last-gasp 2-1 win at lowly Peterborough United.
Barry Fry's men were made to play the second half with ten men after Andy Edwards was sent off two yellow cards just before the break.
The visitors left it until 17 minutes to go to break the 0-0 deadlock when Stephen Brooker put The Valiants in front.
Andy Clarke equalised for The Posh with eight minutes to go but Marc Bridge-Wilkinson was the Port Vale hero as he hit the winner in the last minute to give Brian Horten's side three very valuable points.
Click below for match stats:
Division Two
Barnsley 2-3 Luton
Blackpool 2-1 Northampton
Brentford 1-1 Notts County
Cardiff 2-1 Cheltenham
Chesterfield 1-2 Mansfield
Crewe 1-0 Huddersfield
Peterborough 1-2 Port Vale
Plymouth 0-1 QPR
Stockport 2-5 Swindon
Tranmere 1-1 Bristol City
Wigan 2-1 Colchester
Wycombe 2-2 Oldham
Click here for an updated Division Two table.
