READING’S unbeaten run of nine games in all competitions came to an end after Matt Smith and former Royal Jon Dadi Bodvardsson netted to give Millwall all three points.
The Royals defended well having been on the back foot for much of the game, but were unable to make it 10 unbeaten as Smith’s strike means that Reading drop down two places into 16th in the Championship.
Bodvardsson then came off the bench to score his first league goal in Millwall colours against his former club in the 82nd minute.
Reading made 11 changes from their successful FA Cup third-round replay away at Blackpool, where a youthful looking Royals side navigated their way comfortably into the fourth-round with a 2-0 victory.
The Royals were looking to complete a league double over Millwall for the first time since the 2005/06 season, which proved to be a memorable one as they won the Championship with a record 106 points.
A tame start to the game saw Millwall create the first opportunity after they worked a good move but Mahlon Romeo could not apply the finishing touch as he shot over the bar.
Reading then strode forward as Chris Gunter fired in a cross that was knocked down by the head of Sam Baldock who teed up Yakou Meite, but his shot was well blocked by some brave Millwall defending.
Millwall had an appeal for a penalty as Tom Bradshaw threw himself to the ground, resulting in the unimpressed referee giving him a yellow card for simulation.
Bowen’s side were on the back foot for much of the half as Millwall continued to fire crosses into the box and won seven corners throughout the half, compared to zero for Reading.
But the Royals defended resolutely to shut Millwall out to nullify the impact of their usually aerial dominant side.
Just two minutes before the half time whistle, Rafael flew off his line but was beaten to the ball by Matt Smith who headed just wide with the Reading net unguarded as Liam Moore and Smith collided into each other.
Baldock then had a chance in added time of the first-half but Murray Wallace recovered brilliantly to take the ball off of the toe of the Reading forward just as he was about to strike.
After a sloppy start to the second half, Bowen made two changes to his side just before the hour mark as George Puscas and Jordan Obita replaced Adam and Baldock.
On the 66th minute, Reading created their best chance of the game so far as Blackett swung in an inviting cross towards John Swift but he was unable to convert from just six yards out.
But it was the hosts who took the lead just a few minutes after Reading squandered their chance. Smith put the ball through a crowd of bodies as his shot found the back of the net after clipping the inside of Rafael’s post.
Reading’s final change of the afternoon saw Garath McCleary come on in place of Pele in an attacking substitution.
Millwall then sealed the game in the 82nd minute as Jed Wallace’s cross found Bodvarsson who neatly finished past Rafael.
Reading will look to return to winning ways when they travel away to Nottingham Forest on Wednesday evening.
Millwall: Bialkowski, Romeo, Hutchinson, Cooper, M Wallace, J Wallace, Woods, Molumby, Ferguson, Bradshaw, Smith.
Subs: Fielding, Pearce, Mahoney, O’Brien, Bodvardsson, Skalek, Mitchell.
Reading: Rafael, Gunter, Moore, Morrison, Blackett, Pele, Adam, Swift, Ejaria, Meite, Baldock
Subs: Walker, Miazga, Rinomhota, Obita, McIntyre, McCleary, Puscas.
Goals: Smith 71′, Bodvardsson 82′