Earlier in the week, she scored a goal in the 4-0 victory over Juventus in the Champions League.
Blackstenius scored her goal in the 66th minute, just two minutes after being substituted in.
Arsenal, who have only lost one match in the eight first league matches of the autumn, are in fourth place – one point behind third-place Brighton.
Chelsea, with Nathalie Björn and Johanna Rytting Kaneryd in the starting lineup, won the top match against Manchester City with 3-0 and took the lead in the Super League, two points ahead of City.
The loss was City's first of the season. Chelsea are still unbeaten.
The match seemed to be heading for a goalless draw, but with a quarter of an hour left, Mayra Ramirez scored 1-0, and four minutes later, Guro Reiten scored 2-0 on a corner kick.
