Goals from Casey Stoney and Freda Ayisi proved enough for Kelly Smith’s side to take all three points, with Karen Carney pulling a goal back in injury time from the penalty spot.
However the game will be dominated by another penalty incident after referee Amy Fearn first awarded the hosts a penalty, before rescinding it on the advice of her linesman.
Blues made two changes to the starting line-up which lost to Chelsea last weekend with Emily Simpkins and Kirsty Linnett replaced by Emily Westwood and Jade Moore. Linnett failed to make the squad today having suffered a concussion in the same game.
The hosts started brightly and had the first real chance of the game in the 12th minute when Jess Carter’s ball picked out Remi Allen down the left - the midfielder cut in on her right foot and curled an effort towards the far post, but it drifted just over Emma Byrne’s goal.
Blues were having the better of the possession and the territory in the opening 20 minutes, but went behind against the run of play three minutes later. Rachel Yankey’s initial cross was blocked behind by Chelsea Weston and from the subsequent corner, Japanese star Shinobu Ohno picked out Leah Williamson who headed down for Stoney to fire past Rebecca Spencer from five yards out.
Westwood should have levelled for Blues just two minutes after that goal, but she failed to get a true connection on Carney’s left-wing cross.
The first of Blues’ penalty appeals came a minute before the half-hour mark when Arsenal defender Niamh Fahey appealed to haul down Remi Allen as the ball was played into the box - however, Fearn was unmoved by protests.
With Jo Potter celebrating another call-up to the England squad with a controlling display, Blues looked the team most likely to get the next goal, but could not find an equaliser before the interval.
Two minutes later, controversy struck. A ball from midfield to the feet of Westwood saw the striker roll her defender before she was hacked down. Before Fearn blew her whistle, Allen latched onto the loose ball and was closing down on Byrne’s goal unopposed when she was halted by a whistle which brought play back for a free-kick on Westwood. Blues were incensed by the decision, but further controversy would follow two minutes later.
From the following free-kick, Carney dinked a ball over the top and Jade Moore was adjudged to have been pulled back, with Fearn blowing immediately for a penalty. However, after consultation with linesman Simon Hill, Fearn instead gave a corner kick.
Fired up by the decision, Blues went searching for an equaliser and Allen came within inches of providing one as she charged into the left-hand side of the box before trying to curl an effort into the far corner - but it trickled just wide.
With 56 minutes on the clock, Jess Carter floated a ball over the Arsenal backline which Allen controlled well before firing straight at Byrne with the goal at her mercy.
A succession of Blues corners followed, but they were then hit with another sucker punch. With 20 minutes left, Ohno broke down the left and pulled a ball across the box which found Ayisi at the back post; she cut inside and fired a left-footed effort into Spencer’s top corner.
Blues pressed for a way back into the game and almost had it with six minutes remaining. Potter dinked a wonderful ball over the top of the Arsenal backline and Carney latched on to it, but toe-poked agonisingly wide.
Three minutes into the advertised four minutes injury time, Blues finally got a penalty when Alex Scott was adjudged to have handled a cross. It was a harsh decision on the former Blues player, but Carney stepped up to slot home a consolation against her former club, but it was too little, too late for Blues who stay three points behind Chelsea with a game in hand.
Spencer; Weston, Mannion, Harrop, Carter; Moore (Stringer, 78), Potter; Allen, Carney ©, Lawley; Westwood (Keryakoplis, 78)
Subs: Baggaley, Sargeant, Simpkins, Wellings, Torkildsen.
: Byrne; Scott, Mitchell (Kinga, 78), Fahey, Stoney, Williamson, Bailey, Nobbs, Yankey, Ayisi (Weir, 89), Ohno.
Subs: Chamberlain, Murray, Smith, Sampson, Humphrey.
For more, visit www.birminghamcityladiesfc.co.uk