Wes Thomas, on loan from Bournemouth, turned neatly to convert the opener for Blues four minutes after the break but Chris Taylor's equally well-taken strike levelled matters for the Lions, who face Wigan in their FA Cup semi-final at Wembley next weekend.
It was fit-again winger Taylor who was at the centre of proceedings in the opening 45 minutes.
First he was booked for diving when it looked as though he was brought down by Paul Caddis for a penalty, but unbelievable scenes quickly followed as Taylor's goalbound shot was poked home by Richard Chaplow.
A stunned crowd watched on as the effort was flagged for offside before referee Keith Hill then awarded the goal after discussions with his assistant, only to change his mind once more and subsequently rule it out.
David Forde was beaten just after half-time But as Thomas capped a slick move with a neat turn and low left-footed shot into the corner.
Yet Millwall got the leveller they deserved in the 71st minute as Blues completely fell away.
Rob Hulse got down the left and sent over a cross for Taylor, who took a touch before firing an effort straight past Jack Butland.
With the score at 1-1, Millwall looked the most likely victors as Sean St Ledger headed against the crossbar but both sides went away with a point to remain in the middle of the Championship table.