Northern Ireland had controlled proceedings at Windsor Park but it looked set to be a frustrating evening until Magennis popped up with three minutes remaining.
His close-range finish was a rare bright moment in the second half after Igor Stasevich's deflected strike had cancelled out Jonny Evans' third international goal in the opening 45 minutes.
Victory moves Michael O'Neill's side, who beat Estonia in their opener, to the top of the group after Netherlands was beaten by Germany in Amsterdam.
The host quickly settled into its rhythm and dominated large parts of the opening exchanges, although clear-cut chances were a rarity as quality proved elusive in the final third.
Lone striker Kyle Lafferty cut a frustrated figure as he failed to find room to latch onto enticing deliveries from midfield and his only chance of note came from long range.
However, that shot – which was pushed wide – led to the game's opening goal, Belarus unable to deal with a corner routine as Evans headed home from Steven Davis' front-post flick.
Falling behind seemed to spark Belarus into life and three minutes later they were level as Stasevich's shot clipped Stuart Dallas and looped over the stranded Bailey Peacock-Farrell.
A cagey match failed to produce much of note in the second half as Northern Ireland continued to press without stretching Andrey Klimovich.
Half chances fell the way of Paddy McNair, George Saville and Lafferty but they were all spurned as Belarus defended resolutely.
There was nothing they could do about Magennis' winner, though, as the Bolton Wanderers forward tapped in Stuart Dallas' low cross.