Town suffered their fourth defeat of the season as Millwall ran out 3-1 winners at the New Den. However, despite the loss, the Blues remain top, second-placed Wigan and third-placed Sunderland both losing at home.
Boss Joe Royle recalled Kevin Horlock to the midfield after his one-match suspension and rested skipper Jim Magilton. Darren Currie continued at left midfield.
The Blues had much the better of the first half and Kuqi forced former Blue Andy Marshall into early action. The Finn set-up Darren Bent for a chance but Lions' defender Mark Phillips blocked.
Millwall lost star man Paul Ifill with what looked like a serious injury in the 11th minute, former Fulham man Barry Hayles taking over.
Town continued to press in a one-sided first half and Kevin Horlock went close with a freekick and Richard Naylor headed over.
Marshall saved a Kuqi header, before Darren Bent shot from 20 yards. Soon after, the Blues were denied a penalty when Tommy Miller appeared to be felled inside the box by Peter Sweeney. Neither referee nor his assistant agreed with Town appeals.
Bent missed a one-on-one with Marshall and somewhat surprisingly it was to be the home side who would go in front in the second of five minutes of injury time. The Lions had lost defender Darren Ward in addition to Ifill and one of the referee's assistants had also succumbed to injury.
Millwall's first goal is one the defence collectively will want to forget, De Vos, Naylor and Richards all having ample opportunity to clear before Barry Hayles looped a loose ball over an advanced Kelvin Davis and into the net.
The lead was very much against the run of play, with the Blues in the ascendancy throughout the half.
Wilnis made an important last ditch challenge on Hayles just after the break but there was less impressive defending in the 52nd minute when Daniele Dichio was given the time and space to pick his spot after receiving a cross from David Livermore.
Town boss Joe Royle moved swiftly to change things, bringing on Jim Magilton for birthday boy Matt Richards, now 20, and switching to a 3-5-2 formation.
The Blues got a goal back through Kuqi on 62 when the striker deftly flicked a Miller shot beyond Marshall. The same player might have put Town back on terms shortly afterwards but shot wide from inside the area.
The points were wrapped up in the 79th minute when Scott Dobie latched on to Marvin Elliott's long ball and lashed home.
Late on the Blues gave a debut to loanee Daniel Karbassiyoon, and Dean Bowditch made a brief appearance on what appeared to be an afternoon when Town would lose their position at the head of the table.
However, the later 3pm fixtures saw Wigan defeated 2-1 by George Burley's Derby County at the JJB Stadium and Sunderland lose 3-2 at home to Leeds, former Blue Jermaine Wright crossing for the winning goal.
Town have a chance to stretch their lead when they face Stoke City at home on Tuesday (KO 12.15pm), while Wigan are at Burnley and Sunderland travel to Nottingham Forest. Reading, who leapt above Sunderland with a 3-0 win at home to Watford, travel to Preston.
Town: Davis, Wilnis, Richards (Magilton 56), De Vos, Naylor, Miller, Westlake, Horlock (Karbassiyoon 85), Currie, Bent (Bowditch 88), Kuqi.