Even though the result went against the Dragons, manager Kenny Brown was well satisfied with the performance.
"It was a really good workout for us - we looked good, we were sharp, we were organised," Brown told the club's official website. "We showed a lot of belief in ourselves."
Police had prevented any Millwall fans from travelling to south Wales for the friendly, but the home supporters were treated to a good display by Barry against their Nationwide League Division One opponents.
There was plenty of goal-mouth incident in the first half, with Barry's best chance coming from Gary Lloyd, who saw his free-kick crash off the crossbar.
Nicky Burke had several scoring opportunities that he was unable to convert, while Lloyd had Millwall keeper Willy Gueret diving full length after being set up by Barry debutant Ian Bishop.
Former Manchester City and West Ham midfielder Bishop has signed up for Barry's European campaign.
"Bish made a good debut for us," Brown added. "He can see a pass sometimes five second before everyone else. He's always looking to push the ball forward and create opportunities."
Millwall also kept Barry keeper Simon Rayner busy, with Neil Harris having a 'goal' disallowed for offside, while the Lions striker and Paul Ifill brought good saves from the home stopper.
However, Rayner could do nothing about Charley Hearn's sweetly struck curling free-kick three minutes before the break that put the Lions into the lead.
Both managers made wholesale changes at half-time, but it was Mark McGhee's side that settled first to extend their lead with half-an-hour remaining.
Dave Tuttle and Matt Lawrence combined well to send in a cross to the far post, which was headed down by Cherno Samba for Stuart Booth to stab home from close range.
Barry's best chance of pulling a goal back fell to former Millwall player Jamie Moralee, whose shot from the edge of the box had replacement keeper Tony Warner beaten but went wide of his right-hand post.
"It was a pity that we didn't work their goalkeeper a bit more," Brown said. "It's all very well playing good football, but you've got to get it right in the box as well.
"We constantly missed the target and that's what I'm most unhappy about with the performance."
McGhee, who knows that financial pressures at the Den could see richer clubs cherry-pick his best players, was pleased with his young side's display.
"Everyone knows the situation that we have to work with our young players to boost our squad, and I thought that this was a very good exercise as far as that was concerned," McGhee said.
"Young Matthew Rees made his debut in his homeland Wales, and it was nice for him to have his family there to see that.
"I thought that Charley Hearn was the best player on the park during the first half, whilst Boothy got a goal too and in no way embarrassed himself with his display.
"All in all it was a worthwhile exercise for all of us."
The Dragons travel to Latvia next week for the first leg of their Champions League qualifying tie on Wednesday 17 July, while Millwall have another friendly at Dulwich Hamlet the previous evening.