Brandon Miele's opener for the Magpies was cancelled out by Sanmi Odelusi just before the half time whistle, with the striker left with a simple tap in following a cross from Joe McKee.
With both teams battling to take the points, Wanderers hit the decisive strike midway through the second half as Blakeman slotted home from the spot after Odelusi was fouled.
Despite the win, hosts Newcastle United were crowned champions with Wanderers finishing second with goal difference the only thing separating the sides in the league standings.
Jamie Fullerton’s men can take pride from the result heading back to the North West, with the U21s having won four of their last five league fixtures.
Bolton Wanderers Under-21s: Rob Lainton, Niall Maher, Andy Kellet, Alex McQuade, Cian Bolger, Oscar Threlkeld, Joe McKee, Adam Blakeman, Jack Sampson, Tom Youngs, Sanmi Odelusi
Subs not used: Freddie Woodman, Jamie Sterry, Greg Olley
Newcastle United Under-21s: Jonathan Mitchell, Kevin Mbabu (Alex Nicholson 62), Lubo Satka,Gael Bigirimana, James Tavernier, Rolando Aarons, Michael Richardson, Brandon Miele, Alex Gilliead, Bradden Inman, Jonathyn Quinn (Macaulay Gillesphey 59)
Subs not used: Ben Dennis, Jan Ole Sievers, James Kelly, Aaron Knight, Rob Holding