The 41-year-old's position had become the subject of much scrutiny since the start of the season, with Arsenal only winning one of their first four matches in the Women's Super League season.
The Gunners have also gone without a victory in their first three matches of October, being held to a 0-0 draw by Everton before back-to-back defeats to Bayern Munich and Chelsea in the Champions League and WSL respectively.
Sixth-placed Arsenal are already five points behind leaders Manchester City in the top flight, and Arsenal announced on Tuesday morning that Eidevall had stepped down from his position in the wake of the weekend's loss to Chelsea.
As the Gunners search for a permanent successor to the 41-year-old, assistant coach Renee Slegers - a former Arsenal youth player who joined the coaching ranks last year - will take the reins on a temporary basis.
Edu: 'Arsenal have great respect for Eidevall'
Sporting director Edu paid tribute to Eidevall's work in North London to the official Arsenal website, saying: "We thank Jonas for his commitment to the club and achievements here since joining us in 2021.
"We have great respect for the dedication and commitment he showed to our women's first team and recognise the role he has played in the growth and development of Arsenal Women. We all wish him the very best for the future.
"Our focus will now turn to the process of appointing a new Head Coach, and in the meantime, supporting Renee, as she takes interim charge of the team starting with two important fixtures this week."
Meanwhile, director of women's football Clare Wheatley expressed her "full confidence" in 35-year-old Slegers to oversee operations while the club works to replace Eidevall, adding: "We'd like to say a huge thank you to Jonas for his hard work and dedication to Arsenal Football Club over the past three years.
"Jonas has brought us back-to-back trophies in the last two seasons, together with many memorable moments on the pitch. We wish Jonas and his family the best of health, happiness and success for the future. We have full confidence in Renee to take responsibility for the team in the interim period."
Eidevall's Arsenal record assessed: Was his sacking expected?
Hired as Joe Montemurro's replacement in 2021, Eidevall departs having won exactly two-thirds of his matches in charge of the Gunners, masterminding 80 wins from 120 games at the helm.
The Swede also led Arsenal to back-to-back Women's League Cup triumphs in 2022-23 and 2023-24, as the Gunners upset London rivals Chelsea in the final on both occasions, as well as reaching the Champions League semi-finals in the former year.
However, things quickly turned toxic amid the Gunners' indifferent results in the 2024-25 season, as Eidevall was the subject of heckling from the home crowd in the weekend's loss to Chelsea, and his position was arguably untenable from there.
Arsenal have confirmed that the search for a new permanent head coach is underway, and in the meantime, Slegers will prepare to take charge of Wednesday's Champions League clash with Valerenga before Sunday's WSL fixture with West Ham United.