Central defender Moises's superb 36th-minute header ensured the Portuguese team would finish at least third in Group H which would give them a ticket into the Europa League after the winter break. A higher placing would keep them in the Champions League.
"Our win against Partizan has left us in contention for a berth in the knockout stage and I believe we have every chance of accomplishing the task," Braga coach Domingos Paciencia told a news conference.
"We dominated the game in the first half and took advantage of Partizan's weaknesses and the whole team deserves praise for a spirited performance."
The result completed Braga's double over the Serbian champions after the Portuguese side won the reverse fixture 2-0 and they now have six points from four games, three less than Arsenal and Shakhtar Donetsk.
Partizan have no points after stretching their winless run in Europe's premier club competition to 10 matches and will finish bottom of the group after giving their 30,000 fans nothing to cheer about on a warm evening.
Partizan's fans, who held aloft 30,000 black and white hearts made of paper before kickoff, were in full swing after the restart but their frenetic support seemed to lift Braga and not the home side.
Felipe rescued Braga in the closing stages when he blocked an Almami Moreira effort from a tight angle and fellow midfielder Radosav Petrovic squandered Partizan's last chance with a header just over the crossbar.
"This has been a learning experience for us and I hope we will play better football in the Champions League next season if we qualify for the group stage again," Partizan coach Aleksandar Stanojevic said.
"Mistakes at this level are very costly and we made too many in the first half while we also missed several chances to turn the match around after the break."
