Colchester's hopes were dashed when Graham Kavanagh scored Stoke's winner 12 minutes from full-time.
Fulham are in second place after a 1-1 draw at Oldham. Paul Moody gave Kevin Keegan's side the 50th-minute lead, but Mark Allott equalised for the struggling hosts.
There was plenty of drama at Deepdale, where Preston moved into third place with a 2-0 win over Chesterfield. But the celebrations after goals from Jason Harris (66) and Ryan Kidd (84) were cut short by the sendings- off of Sean Gregan for Preston and Jason Lee for the visitors - both for two bookable offences.
Wycombe Wanderers, struggling at the foot of the table, were grateful for a last-minute equaliser from Danny Bulman after Barry Hayles' 84th- minute goal had appeared to give Bristol Rovers their first away win of the campaign.
Bulman's strike was enough to win the Adams Park club a point after they had lost all four opening matches.
Luton were indebted to Steve Davis for a 3-1 win at Wigan. The defender cleared a Stuart Barlow shot from his own goal line and scored Luton's opener three minutes before the break.
Barlow, the former Everton striker, netted a 62nd-minute equaliser, but two goals in two minutes from Shaun Evers and veteran Phil Gray ensured victory.
Macclesfield continue to struggle at the foot of the table. Ian Hendon's 30-yard free-kick earned the points for Notts County as Sammy McIlroy's Moss Rose side still search for their first win of the campaign.
n The former Chelsea forward Clive Walker became the first man to score 100 League goals and 100 goals in non-League football when he hit Cheltenham Town's opener in the 16th minute of their game against Barrow in the Football Conference yesterday. Cheltenham eventually ran out 4-1 winners.