A goal in either half from Jake Hyde and Ismail Yakubu ended Millwall's interest in the JPT at the first round stage - but the result was almost secondary on a night that saw The Lions' injury woes mount further.
Manager Kenny Jackett must be wondering quite when the dreadful run of luck his squad are experiencing will come to an end.
With no less than eight players sidelined, there seemed to be a little ray of sunshine with the news that skipper Paul Robinson would be making his first start since January.
But Robbo lasted just 37 minutes before appearing to land awkwardly on his left ankle, thus ending his involvement.
Striker Jason Price was the next casualty, before over-stretching for the ball on the halfway line on 53 minutes, and then limping off injured too, taking The Lions tally of walking wounded to an incredible 10.
By that stage, Millwall were already trailing to Hyde's second-minute strike, had bossed the rest of the first-half, but were then simply over-run by a lively, pacey Barnet outfit that thoroughly deserved their victory.
Hyde made the breakthrough with just 123 seconds on the clock. George Friend miscued a clerance, Albert Adomah picked up the ball and produced an inch-perfect cross that Hyde slammed home past debutant keeper John Sullivan.
Millwall recovered from that early shock to go on and dominate the remainder of the opening 45 minutes, but without finding that all-important killer touch in front of goal.
Jimmy Abdou's header was held by Barnet keepr Joe Cole, Price drove into the side netting, Dave Martin and then Ali Fuseini had long-range efforts blocked as Jackett's men piled forward.
The Lions nearly levelled on 20 minutes when a great crossfield ball by Alan Dunne picked out Martin, but the latter's pinpoint delivery was headed over by Gary Alexander from eight yards.
Five minutes later Jack Smith smartly threaded the ball through to Price, he in turn made space before cracking a fierce shot that smacked the underside of the bar, with Alexander inches away from connecting with the loose ball.
Twice Martin sent over low crosses from the left that were agonisingly inches away from the boot of a team-mate as The Lions strived, without success, to level matters before the break.
Barnet could have doubled their tally within seconds of the restart when Adomah - a constant threat down the right flank - produced some nifty footwork to bamboozle Friend, only to see his low drive saved smartly by Sullivan at the near post.
At the other end a thunderous drive by Alexander was held at the second attempt by home keeper Cole as The Lions threatened briefly, but it was Barnet who doubled their tally on 65 minutes.
Adomah, who had twice already gone close with curling crosses, provided a pinpoint corner from the right that was headed back for Yakubu to nod home forcefully from close range.
Hard as Millwall tried to work their way back into the game, it was once of those nights perhaps best forgotten as Jackett's men disappointingly slipped out of a second Cup competition in just eight days, and paid a heavy price on the injury front too.
Barnet: Cole, Devera, Yakubu, Kamdjo (Hart, 90+2 mins), Deen, Adomah, Deverdics, Hughes, Bolasie, O'Flynn (Charles, 78mins), Hyde. Subs not used: Jarrett, Tabiri, Carpenter.
Booking: Adomah (43mins)
Scorers: Hyde (2mins), Yakabu (65mins)

Millwall: Sullivan, Smith, Robinson (Laird, 37mins), Frampton, Friend, Dunne, Fuseini (Bolder, 67mins), Abdou, Alexander, Martin, Price (Grimes, 53mins). Subs not used: Forde, Barron.
Booking: Dunne (33mins)

Ref: James Linnington
Att: 1,623 (away 743)