Jess Sigsworth chased down a loose ball and squared unselfishly for Toone, whose low shot went in via the post.
The Gunners had racked up 29 goals in their opening five WSL wins, but struggled to carve out chances.
Arsenal goalkeeper Manuela Zinsberger prevented further damage with a superb save from Christen Press’ low shot.
United were dealt a blow before kick-off with the loss of England forward Alessia Russo, who is to have surgery on a hamstring injury suffered in training on Friday.
But it was the Reds who created the better chances in a tight game as Joe Montemurro’s free-scoring side failed to create a significant goal threat or build any pressure for record scorer Vivianne Miedema to exploit.
United States international Tobin Heath shot wide of the near post and Toone fired over after a dangerous run from Leah Galton as the pressure built on the visitors.
Just as it seemed United would be frustrated, up popped Toone to seal a fifth straight league win for Casey Stoney’s side and maintain their unbeaten start to the campaign.