Tom Pett opened the scoring just past the half hour only for George Francomb to curl home an equaliser just four minutes later. But Simon Walton struck the winner from the penalty spot with 20 minutes remaining to seal the points in a scrappy encounter at The Lamex Stadium.
Graham Westley made two changes to the side which started the goalless draw at Morecambe with Simon Walton and Chris Beardsley coming in for departed loanee Dave McAllister and Charlie Lee, who dropped to the bench.
It was a bright opening for Boro with Whelpdale hitting the side-netting from a tight angle and both Beardsley and Whelpdale going close with headers inside the six yard box, all within the opening five minutes.
After that frenetic start the game settled down as both sides looked to get used to the pitch and enforce their own style on the game, though it was Stevenage pushing forward.
Sean Rigg forced Day into a low save with a 13th minute effort from distance in the visitors’ first effort of the half before they were indebted to ‘keeper James Shea for denying Boro a 20th minute opener.
Good work by Marriott saw him evade two defenders and find Walton, whose diagonal ball to the back-post was met by Whelpdale, only for his header to force a flying save behind for a corner.
It lead to a sustained period of pressure from Boro with Beardsley nearly latching onto a long pass forward with Shea caught out by the ball holding up on the pitch, before the hosts deservedly took the lead just past the half hour. Much credit goes to Marriott, who did superbly to wriggle his way past three defenders and get his shot off, only for it to deflect into the path of Pett who fired into the roof of the net from six yards out.
Whelpdale dragged a shot wide just three minutes as Boro looked to double their lead only for the Dons to go straight up the other end and fire in a 35th minute equaliser. From a rare counter attack the ball made its way out to Francomb on the right side of the box and he cut back inside and curled a low effort past Day into the far corner, much to the delight of the travelling fans.
With no changes for either side at the break, the second half began with Stevenage on top as a dangerous Pett cross just missed Beardsley, Whelpdale shot a shot deflect wide and Wells saw a looping header claimed by Shea.
Boro’s pressure continued with Marriott seeing a dangerous 51st minute cross evade everyone and Simon Walton curling a free-kick inches over Shea’s bar just before the hour.
Wimbledon eventually came into the half with Akinfenwa putting himself about and helping the Dons win a succession of corners. Fortunately Boro stood strong with Charles outstanding and Wells timing his challenges and headers to perfection.
Pett went close to restoring the lead on 67 minutes when he cut inside and forced a save down low from Shea only for Boro to be awarded a penalty from the resulting corner. The initial delivery found Wells at the back of the box but when he was crudely clattered into seconds after heading the ball back across goal, referee Gibbs had little choice but to give the spot-kick. Defender Shilaja, already on a booking, was lucky to escape a second caution and up-stepped Simon Walton to fire home for 2-1.
Back came Wimbledon and they were certain of a penalty of their own four minutes later when the nippy Azeez went down until a challenge from Charles, but the referee waved away appeals much to the dismay of the visiting fans, players and staff.
A spicy last 10 minutes plus four minutes additional time saw end-to-end action as both sides sought a further goal – Stevenage to kill the game and Wimbledon to salvage a point. At one end Calvin Zola, who looked promising in his 30 minute sub appearance, fired straight at Shea with three minutes remaining when it looked easier to score. Then at the other the whole team showed great commitment and discipline to keep the visitors at bay, who launched wave after wave of attack in the dying minutes.
Victory sees Stevenage complete the double over AFC Wimbledon, extend their unbeaten league run to five and maintain their good home form over the past few months to see them rise to 8th, just a point from the playoffs. Sterner away tests now follow at York and Shrewsbury.
Stevenage: Day, Henry, Wells, Charles, Okimo, Pett, Parrett, Walton, Whelpdale, Beardsley (Zola 60), Marriott (Lee 84)
Subs not used: Beasant, Dembele, Conlon, Deacon
AFC Wimbledon: Shea, Fuller, Goodman, Oshilaja, Kennedy, Francomb, Reeves, Bulman, Rigg (Oakley 80), Azeez, Akinfenwa
Subs not used: McDonnell, Bennett, Moore, Pell, Harrison, Fitzpatrick
Referee: Philip Gibbs
Attendance: 3,306 (602 away)