Junetoft thundered in a shot to make it 1–0 from a tight angle after half an hour of play at Skytteholm in Solna.
In the second half, Olivia Garcia and Ida Björnberg each added a goal.
It feels really damn good, AIK's captain Jennie Nordin told Viaplay.
It was AIK's first match since 39-year-old center back Linda Sembrant, with 160 international caps, announced on Friday that she was pregnant and was ending her football career.
With the victory, AIK consolidated third place in the table, with 18 points after nine matches.
Djurgården is tenth with only eight points.
