Scotland had taken the lead through John Soutter early in the second half, but after a hitting the woodwork three times and seeing a number of other chances spurned, Baker delivered two goals in six minutes to rescue England.
The win keeps them in pole position ahead of the group decider against Ukraine on Thursday, where a draw will be enough to secure qualification to the Finals in July in Hungary.
England U19 2-1 Scotland
UEFA U19 Euro 2014 Qualifying
Elite Round
Pirelli Stadium, Burton
Monday 26 May 2014
In front of England senior team manager Roy Hodgson, Noel Blake’s Young Lions attacked from the off.
Jordan Ibe, the hat-trick hero from Saturday's 6-0 win over Montenegro began the game as he ended the previous – a threat.
The Liverpool man created the first chance of the game as he beat Scotland left-back Stephen Hendrie and fired in a low cross directly into the path of Josh Murphy – but the Norwich City winger blazed his shot high over the bar.
England manager Roy Hodgson watches the Young Lions
Just before the quarter-of-an-hour mark Ibe was again at the centre of things as he picked up a pass from Ola Aina before cutting inside and firing low – only to see his shot well saved by Ryan Fulton in the Scotland goal.
The Young Lions continued to press and were a lick of paint away from taking the lead on 27 minutes. Lewis Baker rolled his free-kick into the path of Harrison Reed and the midfielder fired his low shot inches wide.
England were getting closer but Scotland represented a potent threat on the counter-attack. Christian Walton sprung into action as dived bravely at the feet of Denny Johnstone to prevent the Celtic forward giving Scotland the lead.
But soon after England failed to clear a cross into the box and Scotland captain Adam King’s looping cross drifted towards the back post. Souttar’s gamble paid off as he nodded Ricky Sbragia’s side into the lead.
Denny Johnstone holds off Calum Chambers
England responded well to going behind – and hit the woodwork twice in the space of five minutes. First Akpom struck a post, flicking cleverly over the onrushing Fulton, only to see his effort bounce back of the right upright – before Ibe had a right-footed effort flick the outside of the same post and harmlessly behind.
It was looking as though it was going to be one of those nights – until Baker stepped up to fire the Young Lions level and hauled England back into the game.
After another scramble in the box, the ball bounced off the top of the bar and into the path of substitute Callum Robinson on the left.
England U19 ahead of kick-off against Scotland
The angle was too tight for the Aston Villa man to shoot and he instead squared across the box for Baker, who riffled home at the back post.
Relief turned to delight six minutes later as Baker put England into the lead for the first time in the game. The Chelsea midfielder latched on to another pass perfectly weighted pass from Akpom, and fired home, this time with his left, low past the despairing Fulton to win the game for the Young Lions.
England (4-2-3-1): 1 Christian Walton (Brighton & Hove Albion); 3 Matthew Targett (Southampton), 5 Lloyd Jones (Liverpool), 6 Shay Facey (Manchester City), 15 Ola Aina (Chelsea); 4 Lewis Baker (Chelsea), 17 Harrison Reed (Southampton); 7 Jordon Ibe (Liverpool), 11 Josh Murphy (Norwich City); 9 Chuba Akpom (Arsenal).
Substitutes: 18 Callum Robinson (Aston Villa) for Reed, 58; 14 Ruben Loftus-Cheek (Chelsea) for Jones, 71; 16 Brendan Galloway (MK Dons) for Murphy, 85.
Substitutes not used: 13 Cameron Dawson (Sheffield Wednesday), 8 John Swift (Chelsea), 10 Sam Gallagher (Southampton), 12 Devante Cole (Manchester City).
Goals: Baker 76, 82
Head coach: Noel Blake
Scotland (4-2-3-1): 1 Ryan Fulton; 13 George McLennan, 3 John Souttar, 14 Dominic Hyam, 5 Stephen Hendrie; 16 Adam King (C), 8 Jamie Lindsay; 11 Ryan Gauld, 10 Liam Henderson, 7 Samuel Nicholson; 9 Denny Johnstone.
Substitutes: 15 Charles Telfer for Nicholson) 52; 18 Harry Cardwell Johnstone 69; 2 Ryan Sinnamon for Hendrie 81.
Substitutes not used: 4 Scott McKenna, 6 Darren Petrie, 12 Liam Kelly, 17 Cameron Smith.
Goal: Soutter 51
Bookings: Nicholson 49
Head coach: Ricky Sbragia
Referee: Manuel Ribeiro (Portugal)
Attendance: 835
