Brazilian Lima produced a thunderous 35-yard free-kick to put the hosts one-up, while Luis Aguiar sealed victory late on after a counter-attack.
It was the home side that started the better, looking the more positive with their patient build-up play and passing. Brazilians Lima, Paolo Cesar and Matheus were often at the heart of the action.
Matheus looked lively down the left-hand side and was always willing to get into the box and attack balls coming in from the opposite flank. In the sixth minute Alan almost found him, but his fine cross was just too high.
Cesar trickery led to the free-kick which gave Braga the lead in the 35th minute. Lima stepped up intent on striking for goal - and Partizan keeper Vladimir Stojkovic was only able to get fingertips on the ball as it shot into the top right-hand corner. It was the best moment of the match so far.
Partizan offered little in response in the first half despite enjoying a good deal of possession. The only bright spark for the Serbs came from another Brazilian, Cleo, whose willingness to chase down long balls brought pressure on to their opponents.
The second half started much the same as the first, with Braga in control. Alan came more into the match and in the 57th minute played a smart ball through to Lima who turned smartly on the edge of the box only to fire straight at the keeper.
Partizan showed their determination and began to come back into the match but their attacking moves often came to nothing despite the efforts of Cleo.
Braga put the game to bed in the 89th minute when Alan picked up the ball on the counter-attack and slid a ball through for Aguiar; with only the keeper to beat he unselfishly slid the ball to Matheus to tap in.
It was a deserved win for the Portuguese, who can now begin their fight to progress from the group stages. Partizan, however, face a struggle to claim a Europa League place.