League Cup holders, Arsenal beat Chelsea for the second time this season, a 3-1 win taking the Gunners into the semi-finals.
But it took a couple of late goals, after Karen Carney's 43rd minute opener was cancelled out when Faye White conceded a deflected own-goal from an Aluko shot on 62 minutes.
Jayne Ludlow restored the lead with 12 minutes remaining and Lianne Sanderson made sure six minutes later.
Arsenal Ladies will play Liverpool at home in the FA Tesco Women's Premier League Cup Semi-final.
This match is scheduled to be played on Sunday December 9.
FA Tesco Women's Premier League Cup Semi Final
Watford LFC v Everton LFC
Arsenal LFC v Liverpool LFC