Bowyer, given a free transfer by the Hammers only last January, cashed in with another quality performance to keep the Blues in the top eight.
He was obviously keen to make an impact against his old club and it was a story-book occasion when he notched Blues' 51st minute winner and his sixth goal of the season.
It was another disappointing match for West Ham who even had Mark Noble sent off for a second booking in the second period.
High-flying Blues, with the best home defensive record in the Premier League, maintained their unbeaten record which they stretched to seven games when they recorded their first home win over the Irons since 1985.
West Ham may have gone into the game unbeaten in their last five encounters with City, but they failed to maintain their record despite a barnstorming finish when they laid siege on the opposition's defence.
The Hammers, without an away win since their opening day success at Wolves, had little luck in their bid to change this dismal record on what was manager Gianfranco Zola's 50th Premier League in charge of the Londoners.
Blues' bright start was emphasised by Roger Johnson going close to giving them an early lead when his header from Seb Larsson's corner was blocked by goalkeeper Robert Green.
This early pressure, however, failed to produce a much needed goal and West Ham worked their way back into the game with Alessandro Diamanti twice going close with shots from just outside the area.
These efforts encouraged Junior Stanislas to try his luck and he also tested Joe Hart with a long-range effort which illustrated West Ham's attacking aspirations.
Diamanti, who collected a yellow card for pulling back Benitez, was still the Hammers dangerman with a clever chip which went just wide at the start of the second period.
The stalemate was broken six minutes into the second half when Bowyer scored the vital opening goal against his old club.
Benitez collected a loose ball and fed a pass into the path of Bowyer who coolly slotted home his sixth goal of the season.
The game should have been put well beyond West Ham's reach when Liam Ridgewell failed to convert a Larsson free-kick from close range.
This failure very nearly proved costly as Kieron Dyer hit the post a minute after replacing Guillermo Franco.
Another blatant miss by Cameron Jerome enabled West Ham to remain in the game, but Blues held on grimly for their win.