Yussuff's goal-bound strike took a deflection but sealed the Dons' third npower League Two win of the season.
The winner came seconds after Plymouth target man Rhys Griffiths had levelled after following-in his 89th-minute penalty, initially saved by Dons goalkeeper Seb Brown. The spot-kick was awarded after a foul on substitute Guy Madjo by Yado Mambo.
AFC Wimbledon striker Byron Harrison claimed his fifth league goal of the term to put the Dons ahead in the 13th minute. On-loan Norwich full-back George Francomb crossed in from the right and Jack Midson teed up Harrison to score from close range.
Wimbledon could have forged further ahead but for a superb diving save by Argyle number one Jake Cole, who palmed Yussuff's shot around the post after 26 minutes.
Griffiths had their best first-half effort with a header that flew just wide from Conor Hourihane's corner. Dons keeper Brown made a smart save to keep out Robbie Williams' 32nd-minute free kick from 30 yards.