Four days after Chelsea beat City to win the English League Cup, injury-hit City became the first team to beat Chelsea under coach Sonia Bompastor in her team's 29th game of the season.
Miedema came off the bench at halftime and made the difference in the 60th minute, pouncing on the rebound after Chelsea goalkeeper Hannah Hampton tipped Laia Aleixandri's header onto the crossbar.
Her second was a clinical finish in the 89th after Chelsea had been pushing to level the score.
Fowler played a part in breaking the deadlock, delivering neatly to Aleixandri for the opening goal before being subbed off in the 65th minute.
Fellow Australian Sam Kerr was initially named in Chelsea's squad for the opening leg but was ruled out ahead of the game.
Kerr hasn't played since rupturing her ACL in January last year with her long-awaited return remaining on ice.
Chelsea had one goal by Mayra Ramirez ruled out for offside before Johanna Rytting Kaneryd nearly scored soon after with a shot that hit the bar.
It was the second of four consecutive games between Chelsea and City in the space of 12 days across three different competitions.
They next play Sunday in the Women's Super League before their Champions League second leg on March 27.
In the earlier match Barcelona took a big step toward a third straight Women's Champions League title by beating Wolfsburg 4-1 in the first leg of their quarter-final encounter.
In the first meeting of the two teams since Barcelona beat Wolfsburg 3-2 in the 2023 Champions League final, the Spanish side showed how the gap between the two teams had only grown.
Barcelona took the lead when Ewa Pajor, who joined Barcelona from Wolfsburg last year, pressured defender Caitlin Dijkstra into conceding an own goal as she tried to stop Pajor connecting with Aitana Bonmati's cross in the 26th.
Two goals in the space of three minutes early in the second half took the game further away from Wolfsburg as Irene Paredes scored to finish off a short corner routine before Salma Paralluelo made it 3-0 soon after with a deflected shot.
Wolfsburg had some hope of a comeback when Janina Minge scored a header from a corner in the 79th, but Barcelona's 18-year-old substitute Sydney Schertenleib responded with a curled shot that went in off the crossbar.
