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 in the 70th minute 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.
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.
David Forde was called into action to keep out Nathan Redmond's free-kick before Ravel Morrison fired over after a well-worked move as the hosts made a stronger start.
But confusion soon reigned amid a crazy five-minute spell towards the end of the first quarter.
First, Taylor was booked for diving when he appeared to be brought down by Caddis in the penalty area. But that was nothing compared to the bizarre scenes soon after as Taylor in turn sent a deep cross goalwards which was then helped over the line by Chaplow.
Initially it was flagged for offside before referee Hill spoke to his assistant and instead gave the goal, before then changing his mind 30 seconds later amid protests from blue shirts and once again ruling it out, pointing for a goal-kick.
Jack Butland was called into action as Millwall threatened but, as the half-time whistle blew, the only talking point was the actions of the match officials.
As was the case at the start of the first half, Millwall stopper Forde was forced into action early on, this time to deny Morrison.
But he was unable to keep out Thomas just minutes later as he 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 Butland.
St Ledger, making his full debut, sent a header crashing against the crossbar soon after before substitute Martyn Woolford put just wide.