Paul Cook's side had dropped just two points in their previous six league games but were forced to work hard for their fourth successive victory by a team who started the day in third place.
Gary Roberts opened the scoring for the hosts on the half-hour mark, before defender Sam Hird wrapped up the three points eight minutes after the restart.
Second-placed Oxford United slipped four points behind the pacesetters despite maintaining the division's only other unbeaten record as they could only draw 2-2 at struggling Cheltenham Town.
Chris Wilder's men twice had to come from behind at the Abbey Business Stadium, as Dave Kitson and Johnny Mullins equalised goals from Byron Harrison and Terry Gornell for the hosts.
Fleetwood Town took advantage of Wimbledon's defeat at the Proact Stadium to move into third thanks to a 2-1 home win over Bury.
The visitors went in ahead at the break after Tom Soares had given them the lead in the 28th minute, but second-half strikes from Antoni Sarcevic and Gareth Evans turned the game on its head to give Fleetwood their fourth win in their last five league matches.
At the other end of the table, Hartlepool United claimed their first League Two victory of the season with a 2-1 home success over rock-bottom Accrington Stanley - a result that leaves the visitors with just one point from seven fixtures.
Jon Franks and Andy Monkhouse struck in the first half for Colin Cooper's men, before James Gray ensured that they faced a nervy last half an hour by pulling one back for Accrington.
However, Hartlepool held on for a vital three points that lifts them out of the relegation zone.
York City and Northampton Town are now joint second-bottom of the pile after both succumbed to 2-1 home losses, to Mansfield Town and Exeter City respectively.
Meanwhile, Wycombe and Morecambe maintained their places just below the play-off spots with away victories at Plymouth Argyle and Newport County.
Newport defender Tom Naylor endured a nightmare day at Rodney Parade as he scored two own goals to help Morecambe to a 3-2 success, while Wycombe struck three times in the last 20 minutes to seal a 3-0 win at Home Park.
Elsewhere, Rochdale overcame Torquay 1-0 at Spotland, Burton Albion lost 2-1 at home to Portsmouth and Dagenham and Redbridge beat Bristol Rovers 2-0.
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