The home side gave little away until Romain Larrieu earned a yellow card and conceded a penalty with a foul on Ipswich striker Darren Bent.
Darren Currie converted the spot-kick for a 67th minute lead and then added a second in the 85th minute.
Plymouth pulled a goal back two minutes later when Micky Evans scored but Ipswich held on for the win which, with Wigan not playing until tonight and Sunderland dropping points against Gillingham, allowed the Tractor Boys to move five points clear.
Sunderland could have gone top with the right combination of results yesterday but they could only draw 1-1 with struggling Gillingham at the Stadium of Light.
The day could have been worse for the home side as Darius Henderson gave Gillingham a 15th minute lead at the Stadium of Light.
The home side drew level four minutes later when Chris Brown netted but the Black Cats, who have taken four points from their last four games, will regard the match as an opportunity wasted.
Sheffield United boosted their promotion hopes with a 2-0 win at West Ham.
The Blades were given a helping hand against their fellow contenders when Tomas Repka put through his own goal in the 40th minute.
And they secured the points which took them above the Hammers when Leigh Bromby scored on the hour.
Millwall’s ambitions were dented as they were surprisingly beaten 2-1 at home by bottom side Rotherham.
The Lions opened the scoring through Alan Dunne in the 16th minute but Rotherham equalised when Martin Butler netted two minutes from the end of the first half.
And the Millers earned only their third win all season when Robert Scott netted their second goal in the 69th minute.
The victory was timely as Peter Thorne scored twice to earn Cardiff a morale-boosting 3-0 win over fellow strugglers Nottingham Forest.
All three goals came in the second half with Thorne opening the scoring from the penalty spot after 55 minutes and adding a second four minutes from the end.
Republic of Ireland midfielder Graham Kavanagh netted the third in stoppage time.
Veteran striker Nathan Blake scored his first goal for Leeds following his loan move from Leicester in a 2-1 win at Coventry.
The former Wales international made his debut in the 2-0 reverse against Crewe and gave his latest club the lead in the 28th minute.
David Healy netted a second for the visitors after 65 minutes with Gary McSheffrey pulling a goal back for Coventry in the 82nd minute.
Watford were 2-1 losers at Brighton despite taking an 11th minute lead through Heidar Helguson.
Kerry Mayo levelled for Brighton four minutes later and Leon Knight struck the winner in the 69th minute.
David Connolly converted a ninth-minute penalty as Leicester beat QPR 1-0 at the Walkers Stadium while Burnley were 1-0 winners at Stoke thanks to Gary Cahill’s 79th minute goal.