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.
ADVENTUROUS FORMATION
Partizan started with an adventurous 4-3-3 formation with Pierre Boya and Ivica Iliev either side of striker Cleo but with no one to pull the strings in the centre of midfield, the home side looked bereft of ideas up front.
Braga, who fielded a more conservative 4-5-1 lineup with Brazilian Matheus as the lone striker, looked much livelier and their midfielder Luis Aguiar came close on the half hour when his shot from the edge of the penalty box whizzed over the bar.
With passes going astray and no real pattern to the match, the usually boisterous home crowd were subdued for much of the first half and were completely silenced when Moises scored.
Aguiar floated a free-kick into the heart of the penalty box and Moises rose above his markers to head the ball into the far corner from 12 metres, with Partizan goalkeeper Vladimir Stojkovic caught out of position.
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.
Only a reflex save by Stojkovic, who parried a fierce shot from Matheus, denied the visitors a second in the 56th minute before Iliev scuffed a weak close-range shot straight at Braga goalkeeper Felipe at the other end.
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."
Partizan are at home to Shakhtar in their next match while
