The club from northern city Polokwane finished second from bottom last season and had to win a mini-league involving two second-tier clubs to survive the chop.
They have been a transformed team since while fielding many of the players who struggled to make an impact in their debut Premiership season.
Chiefs moved the home fixture from Soweto to Indian Ocean port city Durban to attract a bigger crowd and were rewarded with a good turn-out.
They took just eight minutes to move ahead with unmarked George Maluleka rifling a lateral pass into the net at Moses Mabhida Stadium.
But a former Chief brought Baroka level midway through the opening half with Zambian Lewis Macha scoring via a glancing header.
The match-winner came just before the hour as Gift Motupa found space in a packed goalmouth to slam the ball past goalkeeper Itumeleng Khune.
Baroka withstood late pressure to claim a fourth Premiership victory this season while drawing three other matches.
They have 15 points, Golden Arrows 13, Cape Town City and Orlando Pirates 12 and Chiefs nine after seven rounds.
Among the pacesetters, only Pirates and Chiefs have won the richest domestic football prize in Africa with the champions pocketing 10 million rand ($740,000/625,000 euros).
Arrows surrendered top spot after being held 1-1 at home by draw specialists Chippa United in another Durban fixture.
Katlego Mashego put Port Elizabeth-based Chippa ahead early in the second half off a free-kick and Zimbabwean substitute Know Mutizwa nodded the equaliser not long after.
Arrows remain unbeaten while it was the fourth consecutive draw for Chippa since former Orlando Pirates star Teboho Moloi became coach.
Thamsanqa Gabuza spared Pirates a second loss in a row by heading a stoppage-time equaliser in a thrilling 2-2 draw at Polokwane City.
Gabuza gave the "Buccaneers" an early second-half lead that was overturned by breakaway goals from Rendani Ndou and Rodney Ramagalela.
But as Polokwane prepared to celebrate, Gabuza punished out-of-position goalkeeper Harold Ndlovu after a long lofted ball into the goalmouth.
Nigerian Victor Obinna scored his first goal for Cape Town City as they defeated Ajax Cape Town 2-0 in a local derby.
Judas Moseamedi wrapped up maximum points two minutes from time for City, whose coach, Benni McCarthy, was part of the Porto 2004 UEFA Champions League-winning side.