George Lebese converted the spot-kick in the 65th minute to hand the Amakhosi their first win in three league matches.
But Steve Komphela’s side was somewhat fortunate to bag the three points as William Twala appeared to have been brought down just outside the penalty area by Highlands Park’s Auguston Leonard.
Twala fell down inside the box, and the referee pointed to the spot. It was a harsh call for the home side, who had dominated the opening 45 minutes and had a number of chances to take the lead themselves.
Jose Garcia on the right and Franklin Cale down the left flank provided good width for Allen Freese’s Highlands outfit, and it was Garcia who found Cale inside the box in the 11th minute.
Chiefs defender Lorenzo Gordinho failed to clear Cale’s header, and the former Capetonian followed up, but a weak shot was straight at Itumeleng Khune.
Highland Park’s best chance came in the 27th minute when Cale whipped in a ball from the left, but his cross was just slightly too high for veteran striker Collins Mbesuma, whose header went over the top.
Chiefs eventually got into the game, with Lebese, Twala and George Maluleke becoming more influential as the match wore on.
Zimbabwean Mitchell Katsvairo had a chance on goal in the 55th minute, but he also shot it over the top, and it looked like the match was heading towards a goalless draw.
But then came the penalty when Twala tried to latch on to a through-ball and was brought down by Leonard, and Lebese beat Highlands Park goalkeeper Tapuwa Kapini with a well-taken goal.
Chiefs finished the stronger of the two teams, but there was some late drama in stoppage time when Khune handled the ball outside the penalty area, which saw Highlands Park awarded an indirect free-kick.
The 9 000-strong capacity crowd willed their team on for the equaliser, and Charlton Mashumba rifled the ball through the Chiefs defence from a layoff with the indirect free kick, but Khune leapt high to his left to make a spectacular save to clinch a much-needed three points for the AmaKhosi.