Anthony Sweeney was the scorer ten minutes into the second half as Hartlepool made more of the game with the wind behind them than the Dons had in the first half.
To make life even more difficult for the Dons late on, they had striker Izale McLeod sent off nine minutes from time, and the ten men were never going to be successful with their late bid for a point.
The game exploded on eight minutes, when 17 players were involved in an ugly brawl just inside the Dons half. After a lengthy conference with his assistants, the referee booked two players from each side, but with punches thrown one or two were lucky not to be sent off.
Helped by the strong wind at their backs, Dons had the better of the first half, the physical presence of Clive Platt and McLeod putting the home defence under a lot of pressure, though keeper Dimi Konstantopoulos only had to save once, picking the ball off Platt's feet on 33 minutes wide on the left of the area.
At the other end, Andy Monkhouse was only inches from connecting with a Richie Humphreys free-kick right in front of goal, while Richie Barker headed just over. But the best home chance came in first-half stoppage time, when Williams hammered a volley against the bar from wide on the left.
With the wind at their backs, it took Hartlepool just ten minutes of the second half to take the lead.
Monkhouse slipped a great ball through the Dons defence and Sweeney took it through to score with a low shot into the bottom corner.
That was only the start of the home chances as they took control of the game, but Dons keeper Lee Harper made a string of tip-top saves to keep the score down, and that meant the Dons were always in with as chance.
Harper's best saves came from another Sweeney shot and a Williams shot, both of them pushed round the post, while he also saved a close-range header from Barker.