Russ Wilcox's side have now won seven of their last nine league games, drawing the other two, after goals from Paul Hayes secured a comfortable victory.
Hayes opened the scoring in the ninth minute and struck again with 16 minutes remaining.
Just below Scunthorpe are Burton Albion, who came from behind to beat Cheltenham Town 2-1 at home and extend their unbeaten league run to nine matches.
Dominic Knowles came off the bench to score twice in the final 18 minutes, the 21-year-old registering his first goals in the Football League after Byron Harrison had put the visitors ahead shortly after the hour mark.
Chesterfield completed a good day for all three sides at the top of the table, thumping struggling Bury 4-0 as second-half goals from Jay O'Shea, Marc Richards and Dan Gardner added to Gary Roberts' 16th-minute opener.
Rochdale, fresh off the back of a surprise 2-0 win over Leeds United in the FA Cup, maintained their momentum with a 3-0 win at Hartlepool United.
George Donnelly opened the scoring five minutes after half-time, with Peter Cavanagh adding a second 13 minutes later and Graham Cummins rounding off the scoring in the final minute.
Rochdale climb above Southend United, who drew 1-1 at Plymouth Argyle, into fourth, while Fleetwood Town are up to sixth after David Ball's goal secured a 1-0 win at Dagenham and Redbridge.
At the other end of the table, rock-bottom Northampton Town's woes continued as they were beaten 2-0 at home by York City following second-half strikes from Ryan Bowman and Wes Fletcher.
Torquay United remain in the bottom two, but only on goal difference after Krystian Pearce and Jayden Stockley scored in a 2-0 win at AFC Wimbledon.
Elsewhere, Bristol Rovers defeated Exeter City 2-1, while Accrington Stanley and Newport County played out a 3-3 draw.
Morecambe and Wycombe Wanderers drew 1-1 and the game between Oxford United and Portsmouth finished 0-0.
