Brown admitted after the weekend's 2-1 defeat at Rochdale that his position is under threat and Howe's first-half goal - his fourth of the campaign - will only serve to increase the speculation about his future.
Tuesday night's 1-0 defeat at Kingsmeadow means the south-west London outfit have just four points to their name in League Two.
The hosts had looked the most likely to score early on when Christian Jolley forced a point-blank save from Michael Poke in the Gulls net.
But, having kept them in the game with impressive saves to deny Lee Mansell and Howe, Dons goalkeeper Seb Brown quickly became the villain when his 35th-minute clearance bounced off the onrushing Howe and into an empty net.
After the break Mansell fired narrowly over from 35 yards before Billy Bodin wasted a good chance as the Gulls looked to add to their tally.
The evening went from bad to worse for the Dons in the closing stages as Jolley was sent off with two minutes remaining - receiving a second yellow card for a clumsy challenge on Mansell.