Mason Bennett grabbed the opening goal for The Lions just after the halfway mark as he prodded home to give them the lead.
Albion fans showed their frustrations towards the end of the match as they halted play twice, throwing a flare and a stadium seat onto the pitch.
Ismael under pressure
He also admitted that he got their system wrong, as Albion were comfortably beaten by Ryan Lowe's outfit.
However, the showing at The Den only three days later proved to have little difference tactically.
Hopeful balls forward were once again prominent, again to no goalscoring avail.
New signing Andy Carroll came straight into the starting eleven following his move to the club on Friday morning.
Carroll proved to be effective in parts as he battled to hoover up some of the expectant lumps forward flung towards him.
But one swallow does not a summer make, and the striker often found himself as the only West Brom player working at 100%.
Albion did come out of the traps the fastest and could've taken the lead through either Carroll or Darnell Furlong, but their attacking intent dwindled as the game progressed.
Ismael now finds himself in the firing line of supporters, with many wishing for the Frenchman to be relieved of his duties.
Millwall end winless run
The Lions had made a dismal start to the new calendar year, not winning a game so far in 2022.
But the hosts put in a display more than worthy of victory and could've increased their tally throughout the game.
The on-loan Sheffield United man had the opportunity to grab the opener as he went one-on-one with Button but shot straight at the 'keeper.
First goalscorer Bennett deserves a lot of credit for his showing in this one, proving to be a nightmare to play against.
He was a constant threat when marauding down the left-hand side, constantly giving Cedric Kipre something to think about and eventually getting a well-deserved goal.
Rowett will undoubtedly take inspiration from the way his side played as they head into their next game against Preston.
Defensive errors became the difference
Before this fixture, Albion had the outright best goals conceded record in the EFL Championship.
Usually so solid at the back, Ismael's side became awash with errors in their defensive line.
The zonal marking used whilst defending set-pieces meant Millwall's opener could be easily scored.
These seemingly uncharacteristic errors at the back will continue to cost them if Ismael persists in keeping games under such fine margins.