Bowyer, who was also the match-winner in Birmingham's previous game against Fulham, struck after just 125 seconds as Wolves crashed to their fifth defeat in eight games.
The victory moved Birmingham six points clear of the relegation zone as they extended their unbeaten run to five games.
That is their best run in the Premier League under the control of Alex McLeish, who was celebrating his second year in charge of the club.
But the problems are continuing to mount for Wolves, who have now collected just three points from the last 24.
Wolves never recovered from Bowyer's fifth goal of the season and remain rooted in the relegation zone - four points away from safety.
To add to the growing worries of manager Mick McCarthy, key winger Michael Kightly, who was sent on as a 32nd minute substitute, lasted just 35 minutes before limping off with another injury - this time to his left ankle.
Birmingham, who put together back-to-back wins for the first time this season, made the perfect start when Bowyer produced a clinical piece of finishing from the edge of the area.
He collected a pass from Sebastian Larsson and took up a quick look up before chipping the ball over stranded goalkeeper Marcus Hahnemann.
It was just the start that Hahnemann let alone Wolves didn't want as the veteran American was making his first Premier League appearance of the season in place of the axed Wayne Hennessey.
But Wolves were ultimately grateful to Hahnemann to ensuring they were still in contention at half-time.
He saved smartly from Larsson before superbly tipping a drive from Bowyer over the bar that had taken a wicked deflection off Kightly.
Wolves were indebted to a deflection off Stephen Ward for preventing Birmingham doubling their lead in the 72nd minute when he blocked a goalbound drive from James McFadden.
In contrast to Hahnemann, Birmingham goalkeeper Joe Hart was a virtual spectator as Wolves toiled in search of an equaliser.
He was only called into serious action once - in the 75th minute when he palmed away a fierce volley from Matt Jarvis.
Wolves' frustrating afternoon was then summed up four minutes from time when unmarked Sylvan Ebanks-Blake headed a David Edward cross wide from just eight yards.