The 2-0 reverse against Scott Fitzgerald's Lions came just a fortnight after a crushing 4-1 loss that sent the Shrimpers spiralling out of the Youth Alliance Cup and Blues boss Ricky Duncan will be hoping that a change of scenery - the next meeting will take place at the New Den - will bring an upturn in fortunes when the sides clash in the FA Youth Cup First Round Proper.
Millwall have adjusted to life in the Football League Youth Alliance after a stuttering start to last season and now represent tough opposition, especially at their Calmont Road training ground. The young Seasiders battled hard throughout to match the hosts' physical presence, but unfortunately could not hold on to record what would have been a worthy point.
Duncan made one enforced change as Callum Whittaker - sent off in the earlier meeting - missed out through suspension, heralding the return of Ade Osifuwa alongside Kane Ferdinand at centre-half. Seven of the starting line-up had featured in the reserve team match at Peterborough United during midweek, although they showed little sign of fatigue during an uneventful start to proceedings.
Southend's organisation at the back made it difficult for Millwall to break them down, with a curling 25-yard effort and a poor finish from a winger when one-on-one with Daniel Bentley all the Lions had to show for their endeavours during the opening 25 minutes.
At the other end, Blues managed to hit their opponents on the break, with Kyle Asante seeing a shot deflected wide after a fine pass from Merrick James-Lewis. However, Jamie Dennis and Marcus Milner were both guilty of wasting good opportunities when they failed to find the final pass.
Bentley did well to gather a difficult skidding free-kick that bounced just in front of him, but the closing stages of the first half saw Blues come closest to scoring. In the 42nd minute, Dennis won the ball well in midfield before finding Asante, who spread play wide to Julian Okai; the first-year scholar connecting with a left-footed drive that smashed against the angle of post and crossbar.
Within seconds, United were on the attack again, this time the impressive John Owinja rampaging down the right-hand side, riding a challenge and cutting the ball back to Harry Crawford, whose scuffed shot was gratefully clutched to his chest by the goalkeeper.
The second half followed a similar pattern, although Millwall found it more difficult to create opportunities in behind the Southend back-line during the early stages. Bentley did have to make two good saves within the first ten minutes of the restart, with Osifuwa also doing his best to distract the forwards.
On 64 minutes another excellent chance presented itself for the visitors as Milner's right-wing centre was glanced just past the post by Asante, with Okai also diving in to attempt to convert. Dennis then warmed the 'keeper's gloves with a searing shot from distance.
There remained warnings about Millwall's ability to cause problems, and defensive indecision between Bentley and Osifuwa almost caused an opening goal, Owinja doing well to cover the danger and set Blues away on the break.
In the 75th minute, Southend were finally undone as a deep cross from the left-hand side was knocked goalwards by a substitute. Two defenders and Bentley all tried to converge on the ball in a desperate bid to keep it out and it appeared that Teddy Nesbitt got the final touch past his own goalkeeper.
Crawford's tenacity won him the ball as Blues fought for a share of the spoils but, following a one-two with midfielder Dennis, he curled over the bar. James Stevens and Dwayne Orachi were introduced as Southend continued to press, although Millwall were unlucky when another sub failed to fire in after Bentley had been forced out of his area to clear.
The second goal duly arrived seven minutes from the end as a home forward controlled the ball on his chest before dispatching a volley into the top right-hand corner of the net from 15 yards out. An injury-time header also struck the woodwork, but three goals would certainly have provided an unfair gloss to the result.
Southend United U18s: Daniel Bentley; John Owinja, Kane Ferdinand, Adetayo Osifuwa; Teddy Nesbitt; Marcus Milner, Merrick James-Lewis (James Stevens 81), Jamie Dennis (Alex Woodyard 86), Julian Okai (Dwayne Orachi 81); Kyle Asante, Harry Crawford.
Substitute not used: George Smith.
League