A first-half strike from former Wanderers loanee Lukas Jutkiewicz gave ten-man Birmingham City the points at Macron Stadium.
The striker pounced onto a free kick late into the half to send the visitors a goal to the good.
And despite Birmingham having Che Adams sent off with just over 20 minutes remaining, Wanderers were unable to make their numerical advantage count.
Phil Parkinson made just the one change from the side that suffered the narrow defeat at Leeds United on Good Friday with Karl Henry returning to the starting XI at the expense of Jan Kirchhoff who was named among the substitutes.
The game opened to a great atmosphere with both sets of fans in fine voice at the Macron Stadium where over 20,000 fans were in attendance for this Sky Bet Championship clash.
On the pitch, the pace was played at a fast tempo during the opening stages with Wanderers shading the possession.
The visitors had half chance 13 minutes into the game when Jacques Maghoma scuffed his effort away for a goal kick after cutting in from the left hand side. The winger ought to have done better given the opportunity he carved open for himself.
Will Buckley had a chance with his head but nodded wide of the far post.
Wanderers’ play was patient and their passing was somewhat intricate. A chance to burst in the box befell to Josh Vela whose attempted cutback into the penalty area was thwarted by the Birmingham defence.
The game was alternating between both halves of the pitch quite frequently, but neither keeper had a shot to save inside the opening half hour.
A Karl Henry defensive clearance fell to David Davis about 30 yards out but the Birmingham midfielder skied his shot high and wide over Alnwick’s bar.
The visitors took the lead five minutes before the break thanks to former Wanderers loanee Lukas Jutkiewicz who was the first player to get to Maghoma’s free-kick. The Birmingham number 10 drove the ball into the roof of the net giving Alnwick no chance.
No changes were made during half-time with Wanderers determined to get a goal to bring themselves back on terms at the earliest available opportunity in front of the 21,097 crowd – Wanderers’ highest of the campaign so far.
Jutkiewicz was looking to add to his tally but his half-hearted left footed volley from just outside the box rolled into the expectant arms of Alnwick.
Flanagan was cautioned for a late foul on Che Adams which resulted in a dangerous free-kick that was cleared by Burke.
Wanderers made their first change after 56 minutes when Craig Noone came on for Derik.
Birmingham survived a huge penalty appeal when Jota appeared to handle Buckley’s cross into the box. Referee Oliver Langford dismissed Wanderers’ vociferous claims much to the chagrin of the home support.
The game turned on its head on the 67th minute when Che Adams was shown a straight red for a late challenge on substitute Noone, who managed to take the resulting free-kick which cannoned off the Birmingham wall for a corner.
Zach Clough came on for the last 20 minutes of the game to replace Buckley.
Clough’s sharpness in the box led to a chance for Le Fondre, whose looping effort landed on the roof of the net.
Wanderers’ final substitution came just moments later with Kirchhoff coming on for Henry.
But David Stockdale in the Birmingham goal was rarely troubled and the visitors held on to claim all three points.