The Dons were edged out in a five-goal thriller as they went toe-to-toe with league leaders Bristol City at Ashton Gate.
However, Wade Elliott put City back in front almost immediately, and despite a late charge from the visitors, they fell just short in a hugely-entertaining clash.
George Baldock and Daniel Powell replaced Jordan Spence and Samir Carruthers in the starting line-up for the clash in Bristol.
Buoyed by his brace in Tuesday’s 2-0 win over Bradford City, Afobe was denied at point-blank range by Frank Fielding on three minutes after Bowditch had headed down Darren’s Potter ball into the box.
However, the Dons found themselves behind a minute later when Agard bundled the ball home from inside the six-yard box after David Martin had saved Mark Little’s initial header.
Baldock’s important block from Joe Bryan’s goal-bound effort ensured the score remained at 1-0 on 11 minutes while, at the other end, Ben Reeves forced Fielding into a smart save from 25 yards, which prompted a good spell of pressure from the Dons.
After recycling a corner, Reeves crossed for Afobe, who headed over from inside the six-yard box as the midway point of the half approached.
Shortly afterwards Powell, a threat going forward, proved his worth defensive with a crucial block from Little as the hosts looked to extend their lead.
Fellow winger Bowditch was also impressing on the opposite flank and an individual moment of magic almost brought the Dons back on level terms but, after expertly flicking the ball over Luke Ayling’s head, his fierce shot was superbly saved by Fielding.
Against the run of play, the hosts went further in front on 35 minutes through Agard’s second of the game - the former Rotherham United man picking himself up after being adjudged to have been brought down in the area by McFadzean to smash the ball past Martin from the spot.
The Dons deservedly pulled themselves back into the game five minutes into the second half courtesy of the lively Bowditch, who calmly slotted home from 12 yards after Fielding had denied Reeves and then Afobe.
Bowditch then cleared Aden Flint’s header off the line from a corner before an injury forced him to be replaced by Will Grigg on the hour.
The men from MK1 continued to dominate possession and territorial advantage but were finding it difficult to create any clear-cut chances, the best opportunity falling to Powell on the edge on the area although his shot lacked necessary power to trouble Fielding.
Robinson replaced Baldock with Spence at right-back on 66 minutes, but the visitors’ next chance came from the opposite flank when Dean Lewington crossed and Reeves rocketed a half-volley inches over the top from 20 yards.
The Dons, though, were level on 73 minutes when fantastic pressing forced Elliott into a short back-pass and Afobe won a 50-50 with Fielding before slotting the ball into an empty net.
However, the hosts were back in front just a minute later as Elliott made amends for his mistake, robbing Kay of possession and finishing well past Martin, who then kept the score at 3-2 with a fine save to deny former Aaron Wilbraham on the counter-attack.
Kay headed a Carruthers free-kick wide and City scrambled away a number of crosses late on as the Dons were denied, perhaps, a deserved point.
Starting XI: Martin; Baldock (Spence 66), Kay, McFadzean, Lewington (c); Potter, Alli; Powell, Reeves (Carruthers 77), Bowditch (Grigg 60); Afobe.
Unused subs: McLoughlin, Flanagan, Randall, Hitchcock.
Goals: Bowditch (50), Afobe (73).
Bookings: Kay, Carruthers.
Attendance: 13, 119 (457 Dons fans)