In a clash where the lead changed hands eight times, Saints guard James Ross led all scorers with 39 points, including five three pointers.
However, it was Tom Ingham who scored five of the defending champion's eight points in the second period of overtime to help put the game to bed.
Down 92-89 with 7.8sec left, Bombers forward Jack Stirling thought he had sent the game into triple overtime when he drilled a deep jumper, only for his foot to be on the line.
The Bombers, who led for the majority of the game, will rue their inability to finish the Saints off, particularly late in the first period of overtime.
Leading 84-81 with 17sec left, all the Bombers had to do was inbound the ball, let the Saints foul them and ice the game from the free throw line.
But the boys in green twice turned the ball over trying to inbound, allowing Damon Cleverley and Ross to drain three free throws between them and knot the game up at 84-84.
Saints guard Liam Aston (12 points) had a chance to win the game on the buzzer, but his three point attempt was no good.
It was a similar story in the fourth quarter for the Bombers, who led 59-46 inside the final eight and a half minutes, but saw their lead evaporate as Ross found his range.
Ross scored a layup and knocked down three shots from beyond the arc to cut the deficit to five, prompting the Bombers to take a timeout.
Bombers guard Olly Smith and forward Max Jablonski each hit a couple of shots following the timeout to give their side a 71-66 lead with 1min 50sec left.
But Cleverley made a tough move to the basket - drawing a foul in the process - for a three point play, before Ross scored a layup and hit a couple of free throws to give his side a 73-71 lead with 30.6sec left.
Bombers swingman Steve Robinson held his nerve from the line to tie the game up at 73-73, before Ross and Cleverley missed last ditch attempts to win the wild game in regulation.
A seventh straight win for the Saints, whose only loss was a week one default, did not look likely when they trailed 22-6 at the end of the first quarter.
But the defending champions showed poise to come barrelling back into the match in the second quarter.
With a second loss to the Saints this season, the Bombers, last year's runner up, are now in fifth place with seven games remaining in the regular season.
In the weekend's other games, Falcons A (5-3) beat Magic A (5-3) 71-60 and Varsity A (4-4) beat Varsity B (0-8) 84-74.
Saints v Bombers
The scores
St Kilda Saints 92
James Ross 39, Tom Ingham 18, Damon Cleverley 15
Bombers 91
Steve Robinson 18, Max Jablonski 18, Jan Verberne 16
Quarter scores: 1st, 6-22; 2nd, 29-30; 3rd, 44-54; 4th, 73-73; OT1, 84-84.
