The result means Amakhosi have finished ninth on the PSL log and therefore will not be taking part in next season's MTN8 Cup competition.
Ernst Middendorp made four changes from the previous game against Free State Stars with Daniel Akpeyi, Erick Mathoho, Teenage Hadebe and Reeve Frosler making their return to the starting line-up.
After a frantic start to the first half, Chippa United lost Tebogo Makobela due to injury nine minutes into the encounter after a challenge from Hadebe.
Chiefs were far ahead of Chippa in terms of dominance, and they were unlucky to see Khama Billiat hit the woodwork in the 11th minute.
At this stage, Amakhosi fans out in the stands were hopeful of their place in the top eight, especially because their team was taking the game to the home side.
However, it was Chippa United who opened the scoring through Manzini after some sloppy defending from Amakhosi.
Phetso Maphanga stole the ball in the Chiefs half and he played a beautiful cross into the area after dribbling past Mathoho, and Manzini beat Akpeyi hands down with an easy tap-in.
Akpeyi, facing his former club for the first time since leaving them, came to Chiefs' rescue minutes later, denying Tercious Malepe what was going to be Chippa's second of the afternoon.
Middendorp was clearly not happy with his team's performance, and his half-time talk was evident because Chiefs came back from the dressing rooms guns blazing.
It wasn't surprising to see him introduce Dumisani Zuma for Hadebe, and perhaps Middendorp should have made this change a bit early as Chiefs were chasing the game.
And that meant Chiefs needed to be more ruthless upfront, and Billiat's left-footed attempt was brilliantly tipped over the crossbar by Chippa United keeper Mbongeni Mzimela.
The Amakhosi technical team was growing frustrated as the game continued, but more so the pressure from the stands was felt by the players as the supporters were visibly unimpressed with the team's showing on the day.
Perhaps, it was time for Chiefs fans to admit that their team was never good enough throughout the season, more so after making several changes to their technical team midway through the term.
Zuma nearly found the back of the net for Chiefs in the closing stages, but Mzimela was on top of his game as he denied the former Bloemfontein Celtic attacker.
In the end, Chippa held on to their lead to register a narrow 1-0 win.
The result saw them beat the drop as they collected 30 points, while Chiefs finished outside the top eight, one of their worst seasons as they couldn't even reach the 40-point mark after 30 games.