The hard-fought victory took the Buccaneers to position eight on the league standings, while the Chilli Boys remain 12th on the table.
The Buccaneers were hoping to bounce back to winning ways in the league following their disappointing 1-1 stalemate with a stubborn Baroka FC side at home in midweek.
Kjell Jonevret, the Pirates coach, made three changes to the starting line-up with Gladwin Shitolo, Thabo Rakhale and Tendai Ndoro being dropped and replaced by Abbubaker Mobara, Thembinkosi Lorch and Thamsanqa Gabuza.
The Chilli Boys were coming off a 3-2 home defeat to Maritzburg United in a league game in midweek and as a result coach Dan Malesela was put on leave by the management of the club.
His assistant Mbuyiselo Sambu took charge of the team and he named South Africa international Diamond Thopola in the starting line-up, while Daniel Akpeyi was surprisingly replaced by Zama Dlamini in Chippa goal-posts.
The visitors applied some pressure on the Buccaneers defence in the early stages of the match with Andile Mbenyane forcing goalkeeper Siyabonga Mpontshane into a decent save with a powerful shot just 10 minutes into the game.
Pirates then took full control the match - attacking in numbers and Mobara was able to find some space outside the Chippa box a few minutes later, and he unleashed a thunderous effort which was tipped over the crossbar by keeper Dlamini.
The home side were oozing with confidence and they deservedly took the lead through their hard-running striker Gabuza, whose low acrobatic effort beat Dlamini at the near-post from Thabo Matlaba's cross to make it 1-0 to Pirates a minute before the half-hour mark.
The goal was able to rejuvenate the Chilli Boys, who tried their luck from range several times, but their attempts could not beat former Platinum Stars keeper Mpontshane in Pirates goal with the half-time break fast approaching.
However, a good move which started in the middle of the park saw Paseka Mako beating the 31-year-old shot-stopper with a powerful left-footed shot to make it 1-1 for Chippa heading into the half-time break.
Swedish tactician Jonevret made a change at the interval with former Chippa midfielder Lorch, who had missed a sitter on the stroke of half-time, being replaced by Pirates fan-favourite Rakhale.
The momentum was with the home side in the opening stages of the second half and they should have doubled their lead in the 52nd minute when Gabuza found himself unmarked inside the Chippa box, but somehow he fired over the crossbar.
However, the Buccaneers continued to press and probe, while looking to penetrate the Chilli Boys defence which was marshaled by Justice Chabalala, who is on a short-term loan deal from Pirates.
Pirates did restore their lead in the 65th minute when Matlaba pulled the trigger from range and former Mamelodi Sundowns shot-stopper Dlamini pushed the ball onto the upright and it went into the back of the net to make it 2-1 to the home side.
The Chilli Boys then gained control of the match with the Buccaneers happy to sit back and launch quick counter attacks as the visitors' defence was left vulnerable, when they pushed forward in numbers in search of the equalizing goal.
Chippa suffered a blow in the closing stages of the match when their captain Thamsanqa Sangweni received his second yellow card and Pirates held onto their slender and they ran out 2-1 winners at home.