Former Bidvest Wits striker Kgaogelo Sekgota made his debut for Swallows, as Maritzburg also gave Travis Graham a first start and preferred Judas Moseamedi up top.
The visitors missed a good chance in the first five minutes after Kwanda Mngonyama picked out Moseamedi in the area, but the midfielder failed to make the opportunity count for his side.
Ernst Middendorp's side were in on goal again a few minutes later when good work from Bandile Shandu and Daylon Claasen teed up Sibusiso Hlubi, but the latter skewed wide of the mark.
Swallows struggled to cope with the onslaught towards the midway stage as Rushine De Reuck headed a corner-kick from Daniel Morgan onto the woodwork.
A substitution from Brandon Trutter's outfit 27 minutes in saw Sammy Seabi coming on for Fawaaz Basadien.
Ten minutes later, the Birds hit the front after winning a penalty kick, which Ruzaigh Gamildien stepped up to convert to send his side ahead into the halftime break.
A double substitution from Maritzburg at the start of the second half saw Hlubi sacrificed for Bongokuhle Hlongwane and Shandu for Tyroane Sandows.
Swallows should've made it 2-0 five minutes into the second half from a run through the area by Sekgota but with just the goalkeeper to beat, the former Wits striker failed to profit.
Middendorp's men were presented a good opening to go level on 56 minutes from a glancing header by Hlongwane off a cross by Daylon Claasen, but the attempt went over.
However, Swalows got the second goal eight minutes later when Gamildien completed his brace from poor defending by the Team of Choice.
An evenly balanced contest ensued in the latter stage of the match, but the Soweto outfit managed to hold their nerve in the end to see out the win.
Swallows: Vries, Mere, Matlaba, Letlabika, Ngcobo, Mokoena, Sekgota, Mthethwa, Basadien, Gamildien, Mbokoma.
Maritzburg: Mwange, Allie, Morgan, Hachi, De Reuck, Shandu, Graham, Mngonyama, Claasen, Hlubi, Moseamedi.
Subs: Barr, Ismail, Sanoka, Sandows, Modise, Hlongwane, Carnell