The 19-year-old took Michael McCrudden's pass near the left channel he fired home an unstoppable finish to make it 1-0.
Toon Beat Smogs 3-2!
A penalty early in the second half made it 2-0 after Nile Ranger was fouled by Boro keeper David Knight before Doninger rolled home.
A double by Jonathan Franks stunned the young Mags to make it 2-2 in the last 15 minutes.
But in stoppage timeDoninger rose highest to glance home Kazenga LuaLua's corner to put Newcastle third in the table and just two points behind leaders Sunderland.
Doninger added: "The atmosphere in the dressing room is good right now.
"Everybody is confident and we're just enjoying each game.
"The season has plenty of games left so we'll see what happens."
NEWCASTLE UTD RESERVES: Krul, Tavernier, Dummett, Doninger, Taylor, Lough, Godsmark, LuaLua, Ranger, Danquah (Spear 83), McCrudden (Williams 58)
Subs not used: Soderberg, Bath, Neary.
Crowd: 433