Stoke took a 15th minute lead through Peter Thorne and added a second through Paul Connor just after half-time.
Marc Bircham gave Millwall hopes of repeating last week's comeback against Walsall when he scrambled the ball home after 75 minutes, but a Graham Kavanagh penalty six mintues from time guaranteed Stoke the points.
An injury-time goal from the Welsh international striker Simon Haworth gave Wigan a 2-1 victory over Bristol City at the JJB stadium. Tony Thorpe's 72nd-minute penalty seemed to have earned the visitors a point, before Haworth struck late on.
Chesterfield's striker David Reeves netted all four goals in the 4-2 win against newly-promoted Cambridge United, two of them coming from the penalty spot, to earn his side their first points of the season.
Reeves' former club Preston relinquished the last remaining 100 per-cent record in the division despite taking the lead against Wycombe at Adams Park. Kurt Nogan gave Preston the perfect start, but Wycombe's prolific striker Sean Devine equalised five minutes from time.
Notts County are the early pace-setters after two goals from Mark Stallard and another from Craig Ramage gave them a 3-0 victory over promoted Scunthorpe.
The Gillingham manager, Peter Taylor, was sent off in the second half at Blackpool. And things got worse for the former England Under-21 manager as John Murphy grabbed a 75th-minute equaliser in a 1-1 draw.
Ian Lawson scored the quickest goal of the season so far as Bury drew 2-2 at home to Brentford. It came after just 13 seconds.
Jason Roberts, Bristol Rovers' in-form striker, added to his growing reputation withwith the 60th-minute winner as Rovers beat Oxford United 1-0 at the Memorial Ground, while Reading slipped to a 2-1 home defeat against Luton.
In the Third Division, Rochdale hit the summit with a 3-0 win at York City.
Graham Lancashire (33), Clive Platt (56) and Graeme Atkinson (61) ensured a comfortable victory and extended the Spotland side's 100 per-cent start to the season.
Peterborough also maintained their unblemished start to the campaign as they consigned Tommy Taylor's Leyton Orient, play-off finalists last season, to their third straight defeat of the campaign. Matt Etherington and Steve Castle scored the goals in Peterborough's 2-1 win, with Matt Lockwood replying.