The 34-year-old midfielder, who had two spells at Upton Park, earned Ipswich a second win in three games to hand manager Paul Jewell, who turns 47 on Wednesday, an early birthday present.
Bowyer registered his first goal for the club, tapping into the net after Keith Andrews had seen his header from Jimmy Bullard's corner hit the post.
It ended the Hammers' seven-game unbeaten run in the Championship as the hosts, who have made their best start to a league season in 28 years, also squandered the chance to move top of the table.
Town made a bright start and had an early opportunity to take the lead but Michael Chopra's close-range effort was saved with his feet by Hammers goalkeeper Robert Green.
The home side were being pegged back by the imposing visitors and Bowyer was inches away from celebrating a goal against his old club when his 12-yard effort hit the post.
Henri Lansbury, who spent last season on loan at Town's East Anglia rivals Norwich, was fired up for the game and, after being booked for a foul on Carlos Edwards, he fired a 30-yard shot off target.
It seemed to spark the Hammers into life and they came close again shortly afterwards but Abdoulaye Faye could not keep his header down from David Bentley's corner.
Ipswich responded and a Grant Leadbitter strike from 18 yards forced Green into another save.
West Ham made a better start to the second half and within five minutes Carlton Cole tested Town goalkeeper David Stockdale with an 18-yard strike before Joey O'Brien cleared the crossbar with an effort just outside the penalty area.
Another long-range Leadbitter strike was easily dealt with by Green before an excellent block by Town defenfer Aaron Cresswell kept out a Kevin Nolan header from close range.
Play was switching from end to end and the next opening arrived for Town striker Jason Scotland but he could not find the target with his 25-yard strike and was again wayward moments later from similar range.
With eight minutes left, Green was at full stretch to tip Cresswell's 30-yard free-kick over the crossbar.
Just as the game was seemingly heading for a goalless draw, Bowyer popped up to stun the Hammers.
Stockdale was called upon to save from Jack Collison in injury time but Town secured a third successive clean sheet, the first time they have achieved that feat since March 2005.