Miedema put Arsenal ahead early in the second half with her 13th goal of the season to become the first player in WSL history to score against all the teams she has faced.
Katie McCabe sealed the victory from the penalty spot as Arsenal found their way back to victory after their 1-1 draw with Tottenham last weekend.
Arsenal, who also hit the bar twice as they headed for victory at Leigh Sports Village, appear poised to go the distance with Chelsea in the title race this season
This victory against Manchester United allows the Gunners to enter the international break at the top of the standings, ahead of Chelsea who remains on their heels.
United were beaten 6-1 by Chelsea in September and their second loss of the season leaves them within 10 points of Arsenal.