The former Oldham player notched his second goal of the season to the delight of manager Chris Powell who has recently bemoaned the lack of goals from his side.
Building upon their strong defence Charlton carved out a vital 1-0 away win to give them fresh hope of an improvement in their fortunes.
Birmingham, however, are now without a win in their last five games and the pressure is beginning to tell as they continue to free-fall into a relegation dog-fight.
Manager Lee Clark now faces a difficult time trying to lift his young side in what is proving a troublesome time on and off the pitch for Birmingham.
With Charlton's defence strong, Clark's side always had a difficult time trying to gain the upper hand.
Charlton were always a danger on the break and this proved to be the major difference when Stephens scored their 56th minute match winner.
It was yet another huge disappointment for Birmingham after their League Cup defeat on penalties at the hands of Stoke.
There was some early urgency in the Birmingham side to make amends but it was to no avail.
Charlton's defence, which has now maintained clean sheets in their last four games, was in no mood to concede although they had an early scare when a Dan Burn goal was disallowed for an infringement on the part of Lee Novak.
As a result this game between two struggling teams near the foot of the division became a battle to gain the upper hand.
Birmingham maintained a strong attacking policy but Charlton's resolute defence was generally not fully tested.
Michael Morrison and Dorian Dervite were stalwarts as they accorded Lee Novak and Nikola Zigic few goal opportunities.
The one occasion that Novak had a shot on target goalkeeper Ben Hamer made a super save diving low to his right.
Charlton's only real chance in the first half fell to Stephens late in the first half but his effort lacked power and Darren Randolph made an easy save which summed up a low key and disappointing first half.
Stephens, however, more than made amends early in the second period when he notched a rare Charlton goal in the 56th minute.
Randolph parried an effort from Cameron Stewart but Charlton had their tails up and following a cross from the left Bradley Pritchard nudged the ball into the path of Stephens who, with an open goal at his mercy, made no mistake from close range.
It is only Charlton's 10th goal of the season and could be the goal to kick-start their climb up the table.
Although Birmingham made a double substitution sending on Shane Ferguson and Peter Lovenkrands for Demarai Gray and Novak they still struggled to break down Charlton.