The Magpies went ahead through French striker Wesley Ngo Baheng, who took his tally to four in three reserve team outings.
However, the 20-year-old's strike wasn't enough as Boro levelled through Didier Digard – a former team-mate of Baheng's at Le Havre.
Digard, who was making his return from injury, was one of a number of players with first-team experience among the Boro squad, which also included Justin Hoyte, Seb Hines and Jonathan Grounds.
A volley by Jonathan Frank on 66 minutes was enough to secure the win for the Smog Monsters.
MIDDLESBROUGH: Steele, Hoyte, Hines, Smallwood, Grounds, Porritt (Williams 67), Digard, Pilatos, Park (Corker 67), Franks, Martin (Saiko 72). Unused subs: Ripley, Shead.
NEWCASTLE: Alnwick, Morris, Lough, Newton, Tozer, Kadar, Adjei, LuaLua (L Henderson 89), Ngo Baheng, Ameobi (Spear 85), Danquah (Folan 66). Unused subs: Johnson, J Henderson.