Ernst Middendorp made mass changes from their loss against Chippa United last weekend, as he gave Lebogang Manyama his first start since returning from injury while Kabelo Mahlasela, Daniel Cardoso and Siphosakhe Ntiya-Ntiya also returned.
The game was lively in the early stages with the Rockets showing bravery by knocking the ball around and being able to rotate it for a considerable spells.
Dan Malesela's charges carved out the first chance of the match in the 20th minute after a surging attack on the left channel, where Thembinkosi Mbamba nearly opened the scoring with a diagonal shot that sailed over the bar.
Amakhosi were struggling to get their rhythm going forward and after half-an-hour they were yet to test Galaxy shot-stopper Ludwe Mpakumpaku in goal.
Chiefs' first real chance at goal came three minutes before the break through Teenage Hadebe's header that sailed over the bar from a set-piece, before Bernard Parker had an effort cleared off the line minutes later.
Middendorp's troops were fired up in the early moments of the first stanza as Manyama came close to breaking the deadlock three minutes inside the second half with a left-footed lob that sailed just wide of the upright.
Amakhosi increased their intensity towards the hour-mark but they were yet to carve out clear-cut chances despite showing urgency to draw first blood, which prompted Middendorp to withdraw Manyama for Dumisani Zuma, who had two cup goals to his name this season.
With the game getting tense and frustrations rising, Willard Katsande had a glorious opportunity to find the breakthrough for Chiefs with seven minutes remaining, but the Zimbabwean fired horribly over the crossbar.
Amakhosi conceded a penalty in the last minute of the match after Hadebe brought down second-half substitute Zakhele Lepasa, who dusted himself off to step and send Bruce Bvuma the wrong way to seal the cup for Galaxy.
As a result, Galaxy became the first side from the National First Division to win the Nedbank Cup titile.
Chiefs: Bvuma, Hadebe, Cardoso, Moleko, Ntiya-ntiya, Mahlasela, Katsande, Dax, Manyama, Billiat, Parker.
Subs: Petersen, Mphahlele, Castro, Maluleka, Zuma, Zulu, Frosler.
Galaxy: Mpakumpaku, Aubaas, Dube, Mashego, Nyama, Chaine, Mbamba, Bodibe, Nduli, Mdlinzo, Ndlovu.
Subs: Phungwayo, Myataza, Shangase, Lepasa, Abrahams, Ndlovu, Ngidi.