The Toon teenagers trailed in the first-half of their opening Group F clash at the Magpies' Little Benton Academy following Elias Mansor's deflected effort.
Sixteen-year-old winger Matheos Ferreira drew thew hosts level towards the hour mark, firing home from Jake Durrant's cross, but the spoils were ultimately shared on Tyneside.
Joe Brayson went close to firing the young Magpies into the early lead as the teenage forward, son of former Magpies forward Paul, saw a close-range header from Ferreira's teasing cross wide of the target.
Rory Finneran, making his Newcastle debut at under-18 level following his move from Blackburn Rovers, completed a driving run before the Republic of Ireland Under-17 international threaded a neat pass into Ferreira's path but his resulting effort struck the side-netting.
In the 22nd minute, Millwall took the lead through Mansor. After the United defence were unable to clear their lines from a corner, the Lions defender's strike at goal took a slight deflection before flying into the net.
Newcastle ought to have drawn level shortly after conceding as striker Kacey Wooster's initial effort was parried by Millwall goalkeeper Jakob Przewoźny before the 17-year-old denied Ferreira from point-blank range, turning the rebound out for a corner.
Adam Harrison, who signed his first professional contract with his boyhood club last month, produced an important save to prevent Elidon O'Boyle doubling the visitors' lead, standing tall before blocking the striker's placed attempt at goal.
United's youngsters maintained their push for an equaliser in the second-half as Sean Neave, a representative of England at under-17 level, completed a surging run from distance before the 17-year-old's cross-cum shot from the left byline was turned out for a corner by Przewoźny.
In the 59th minute, Newcastle drew level through Ferreira, who latched onto Durrant's in-swinging cross from the left flank before drilling a first-time strike into the net.
Millwall went close to quickly regaining the lead as O'Boyle intercepted Harrison's pass from his own box but lashed his effort over the crossbar.
Durrant almost turned from provider to goalscorer as the 16-year-old left-back's fierce effort, directed towards the front left-hand post, was pushed away by Przewoźny.
Newcastle United Under-18s: Adam Harrison, Ezra Tika-Lemba (Guy Bloomer 65), Henry Johnson (Luke Craggs 46), Logan Watts (c), Jake Durrant, Rory Finneran (Matthew Taylor 46), Jude Cogdon (Mo Waddani 85), Matheos Ferreira, Joe Brayson, Sean Neave, Kacey Wooster.
Subs not used: Tyler Jones.