Emblen, who also scored the winner when the teams met at Milton Keynes in December, earned Walsall their first victory of the year with his 27th minute strike.
Walsall had gone 11 league and cup games without a win before Emblen struck to earn Colin Lee's side a priceless success.
But for Wimbledon their woe continues. They have now lost their last nine games - scoring just one goal in the process as they wait for the inevitability of relegation.
As well as picking up a victory, Walsall were also boosted by the return of skipper Paul Merson.
The former England star made his comeback after a month in America having treatment for his addiction to gambling with a substitute appearance.
Emblen fired the game into life to cap a spell of Walsall pressure.
The Saddlers had twice gone close before he struck with Jorge Leitao lifting his volley just over the bar and Emblen being denied by a save from debutante goalkeeper, Scott Bevan.
But 6ft 7ins giant Bevan, who has moved to Wimbledon on-loan from Southampton for the rest of the season, was powerless to prevent Emblen firing Walsall ahead after 27 minutes.
Emblen's strike was a personal disaster for the Wimbledon central defender Rob Gier.
Gier tried to take his time before clearing the ball but Emblen caught him in possession.
He then raced forward and into the area before drilling his low shot past the outstretched right hand of Bevan.
His strike looked set to see Walsall take a stranglehold on affairs but they struggled to build on their advantage.
Wimbledon posed more a threat as the game wore on and they threatened to snatch a point through substitute Michael Gordon after 63 minutes.
He was unmarked in the area and it needed a smart save from keeper James Walker to pluck his goalbound shot out of the air.