The Dons came out on top in a seven-goal thriller at Vale Park to book their place in the second round of the FA Cup.
Karl Robinson made five changes for the fixture in Staffordshire with Tom Flanagan, Mark Randall, Baker, Samir Carruthers and Will Grigg coming into the starting XI. Dele Alli was rested, Antony Kay and Darren Potter suspended, Dean Bowditch ill and Daniel Powell was unavailable as his partner had just given birth.
The Dons settled the better of the two teams and Grigg brought a save out of Chris Neal as early as the fourth minute after cutting in from the edge of the area.
Despite operating in a deeper than usual role in central-midfield, Ben Reeves was still getting forward well and he rattled the bar with a rasping 25-yard effort three minutes later – Baker couldn’t turn home the rebound.
Nice link-up play between Jordan Spence and Benik Afobe down the right then presented Grigg with a chance shortly afterwards, but his shot was well blocked by Ryan McGivern.
Completely against the run of play and on their first attack, Vale took the lead on 10 minutes when Ben Williamson’s weak shot from Chris Birchall’s cross took a deflection of Spence, giving David Martin no chance.
The men from MK1 responded well, with Grigg lifting a 20-yard effort just inches over the top before some last-ditch defending from McGivern denied Afobe and Baker at the back post from Grigg’s cross.
Robinson’s side continued to dominate proceedings as the clock ticked past the midway point of the first half with the front six looking dangerous, but they were finding it to difficult to test Neal.
However, the Dons’ pressure finally told on 31 minutes as Afobe latched on to Randall’s inch-perfect through-ball and coolly slotted home to deservedly bring the visitors level, taking his tally to 14 goals for the season in the process.
Baker, a constant threat from right wing, then fired the Dons in front with a fine left-footed finish from 20 yards nine minutes later – his first goal for the men from MK1.
But they were forced to go in at the break on level terms as Dany N’Guessan turned smartly and drilled under Martin from 12 yards following a cross from the right.
Referee Breakspear waved away strong penalty appeals 53 minutes in when Afobe appeared to be brought down in the Vale area which, if awarded, would have also resulted in a red card.
However, the Dons were awarded a spot-kick five minutes later when Carruthers was tripped by Williamson after some smart build-up play, and Afobe made no mistake from 12 yards, sending Neal the wrong way to tilt the pendulum back in the visitors’ favour.
Looking to atone for his error, Williamson hit the post with a header from Birchall’s right-wing cross on 63 minutes, but the offside flag was raised anyway should Vale have scored from the rebound.
Green made a welcome return to first-team action on 73 minutes, replacing Carruthers in midfield, and marked it with his first goal for the Club as the clock ticked into the final 10 minutes, tapping home Afobe’s cutback from six yards at the back post.
However, a second for N’Guessan just two minutes later made things interesting, the former Leicester City man finishing from close range after Mark Marshall’s initial effort had come back off the post.
Robinson handed Kabongo Tshimanga his debut in the final stages of the game as the Dons held on for a deserved victory to ensure their place in Monday night’s draw.
Starting XI: Martin; Spence, McFadzean, Flanagan, Lewington (c); Randall, Reeves; Carruthers (Green 73), Grigg, Baker; Afobe (Tshimanga 90+4).
Subs not used: McLoughlin, Hickford, Hodson.
Goals: Afobe (31 & 58), Baker (40), Green (81).
Bookings: Carruthers, Flanagan.
Attendance: 4,120 (314 Dons fans).