The young Magpies fell behind at the Select Car Leasing Stadium following Jacob Borgnis' first-half opener for the Royals before two red cards were shown shortly after the hour mark, with John Ryan receiving a straight red card after appearing to kick Magpies striker Sean Neave, who picked up a second yellow card following the altercation.
Newcastle's second-string, though, recorded back-to-back league draws as Miodrag Pivaš, who joined the Magpies from Serbian SuperLiga side FK Jedinstvo Ub in the summer of 2024, levelled for the visitors in the closing stages, the Serbian defender's first goal for the club.
Adam Lawrence made three changes from Monday's 3-2 defeat against Norwich City as Leo Shahar replaced Harrison Ashby at right-back while Scotland Under-21 international Charlie McArthur and Mohamed Waddani, the latter making his debut at under-21 level, replaced Pivaš and Kyle Fitzgerald respectively.
Newcastle found themselves under early pressure within the first 90 seconds of the league encounter, with Magpies goalkeeper James Taylor pushing away Ryan's free-kick, despite the Kettering-born shot-stopper conceding the set piece after being adjudged to handle the ball outside of his penalty area.
In the 16th minute, United's second-string trailed through Borgnis as the Royals skipper connected with Tyler Sackey's corner before flicking the ball beyond Taylor, with the goal standing despite the linesman appearing to flag.
United's youngsters were fortunate not to fall further behind before the half-time break as Sackey's cross was diverted wide by Ryan at the back post.
In the second-half, both teams were reduced to ten men as Neave received his marching orders. Booked minutes prior, the Winlaton-born striker was involved in an altercation with Ryan on the right flank, with the Royals defender dismissed after appearing to kick out at the 18-year-old forward but the latter, to the visitors' disbelief, was shown a second yellow card.
Newcastle equalised in the 75th minute as Pivaš, introduced from the substitutes' bench towards the hour mark, netted his first goal for the club with a smart close-range finish.
Taylor prevented Sackey from regaining Reading's lead in the third minute of stoppage-time as the 19-year-old 'keeper, who made his full senior debut for National League South side Hemel Hempstead in August 2023, held the Royals midfielder's strike from the edge of the box.
Newcastle United Under-21s return to Premier League 2 action on Sunday, 5th October when hosting Tottenham Hotspur at Whitley Park (kick-off 4pm BST).
Newcastle United Under-21s: James Taylor, Leo Shahar, Dylan Charlton (Kacey Wooster 72), Charlie McArthur, Cathal Heffernan (c), Scott Bailey (Joe Brayson 46), Alfie Harrison, Rory Finneran (Fraser Harper 81), Sean Neave, Anthony Munda, Mohamed Waddani (Miodrag Pivaš 59).
Subs not used: Will Anderson.