Fulham, unbeaten in their previous five games, were off-colour in the awful conditions and struggled to find their form against a determined Birmingham side that is rapidly adjusting to life in the Premier League.
Bowyer's opportunist 16th-minute goal revived memories of his days at West Ham United, and it was the difference between the two teams as Birmingham produced another solid defensive performance to keep their fifth clean sheet of the campaign.
In the torrential rain, Birmingham delighted their fans with some impressive attacking play as they put Fulham under strong pressure.
The speed of Christian Benitez and Cameron Jerome was always going to be a handful and so it transpired. The only problem for Fulham was that they seemingly concentrated upon the threat of the two strikers and totally forgot about the goalscoring ability of Bowyer.
Bowyer demonstrated great coolness when he latched onto a subtle pass from James McFadden in the 16th minute.
Bowyer timed his run perfectly to race through Fulham's defence before gently lofting the ball over the head of the advancing Mark Schwarzer for his fourth goal of the season.
Surprisingly there was very little real pressure from the Fulham attack. Bobby Zamora wasted an early chance and then disappeared from the radar as Birmingham's up and coming central defenders, Roger Johnson and Scott Dann, were well in control.
The closest Fulham came to a first-half equaliser was just before the break when a Brede Hangeland header skimmed just over the bar.
Zoltan Gera also went close 15 minutes into the second half but the Hungarian couldn't quite control his shot and it went over the bar.
Birmingham struggled to regain their first-half momentum and this enabled Fulham, again lacking the services of skipper Danny Murphy, to build up some promising attacks with former West Brom skipper, Jonathan Greening, emerging as their midfield general.
In this spell Stephen Kelly, the former Birmingham defender, broke through and proved a fine cross from which Clint Dempsey headed wide.
Kelly's reward for some fine work was to be substituted by manager Ray Hodgson, who sent on Republic of Ireland international Damien Duff in an attempt to inspire the elusive equaliser.
As usual, Birmingham had to survive a hectic spell as Fulham bombarded their goal but with no success.