The Group E fixture was decided by a single goal on the stroke of half-time as Megan Connolly struck for Hope Powell’s team.
Lucy Quinn and Emily Whelan had Blues’ best opportunities at St. Andrew’s in what was the first of three Group E matches.
Scott Booth made just the one change to the team which started Sunday’s 1-1 draw on the road at West Ham United. Veatriki Sarri was recalled from the off in a switch with Ireland international Emily Whelan.
Before either side was able to create a chance on goal the hosts were forced into an early change. Rebecca Holloway was withdrawn injured, with the versatile Libby Smith entering from the bench after just 12 minutes.
And this was followed by the game’s first significant openings, as Brighton did just about enough to firstly deal with a dangerous in-swinging Lucy Quinn corner and then usher the loose ball out of the box.
The midfield Quinn was again causing problems soon after and tested the handling of Megan Walsh, but the Seagulls’ stopper managed to keep hold of the 30-yard strike.
At the other end, with nearly half an hour played, Marie Hourihan was well placed to deny the visitors. The stopper was sharply down to block Katie Robinson's shot as she tried her luck from the angle.
But the Blues stopper could do nothing to prevent Brighton from taking the lead after 44 minutes. Connolly reacted quickest as the home side could only half-clear, accurately steering the ball into the far corner.
Half-time: Blues 0-1 Brighton & Hove Albion
Blues started the second period brightly and perhaps should have made more of an opportunity created by Lucy Quinn. The summer arrival burst forward and unselfishly opted to pass, only for the ball to evade Harriet Scott as she raced into the box.
But still searching for an equaliser, Booth turned to his bench and introduced Whelan, with the Ireland international almost instantly seeing a half-volley blocked as the ball sat up from a corner.
Compatriot Eleanor Ryan-Doyle was also called upon with less than 20 minutes remaining as Blues looked to their attacking arsenal for a way back into the encounter.
And a leveller looked close when Walsh failed to gather as she came claiming an aerial free-kick from off her goalline. However, the Brighton defence did just about enough to block a couple of Blues attempts and sneak the victory in B9.
Brighton’s goal came at a critical time, shortly before the interval, and blotted what was an otherwise near faultless defensive copybook.
Defeat does not spell the end of Blues’ Conti Cup adventure this season, with group fixtures against West Ham United in the West Midlands and away at London City Lionesses still to come.
Blues Women: Marie Hourihan, Jamie Finn, Louise Quinn (captain), Gemma Lawley, Rebecca Holloway (Libby Smith 12), Harriet Scott, Lucy Whipp (Eleanor Ryan-Doyle 71), Veatriki Sarri (Emily Whelan 58), Lisa Robertson, Lucy Quinn, Jade Pennock.
Unused substitutes: Emily Ramsey, Cecilie Sandvej, Abi Cowie, Sophie Phillips, Freya Clarke.
Bookings: Lucy Quinn 80.
Brighton & Hove Albion: Megan Walsh, Emma Koivisto, Felicity Gibbons, Maya Le Tissier, Aileen Whelan, Megan Connolly, Geum-min Lee (Maisie Symonds 46), Rinsola Babajide, Ellie Brazil, Victoria Williams (captain) (Danique Kerkdijk 70), Katie Robinson.
Unused substitutes: Frances Angel, Inessa Kaagman, Libby Bance, Kayleigh Green, Danielle Carter, Emily Simpkins, Faith Nokuthula.
Bookings: Williams 60.
Referee: Lisa Benn
NEXT STEPS: The season pauses for its second international break ahead of domestic action resuming in the Barclays FA Women’s Super League at the start of November. Next month begins with the hosting of Reading, with a Second City derby at St. Andrew’s to follow.