Wandile Duba opened the scoring at the Moses Mabhida Stadium after 31 minutes and Mfundo Vilakazi sealed the result with his goal after 83 minutes.
The result left Magesi rooted to the bottom of the standings with 14 points from 21 games.
Reflecting on the result, Freese explained that his team played well and had chances to win the tie, but ultimately made too many mistakes.
"I think in the first half we had good opportunities; we could've scored maybe a goal and take it from there," Freese told SuperSport.
"But individual mistakes it's costing the team, individual mistakes not as a whole. Too many loose balls, not marking properly," he said.
Magesi had recorded a 2-2 draw with Chippa in their previous game and will look to bounce back from this defeat at home to Marumo Gallants after the international breal on April 7.
"I thought the first half we did really well, second half - I thought when we made the changes, maybe we fell too pieces a little bit, I don't know but too many mistakes cost us the game," added Freese.
"Well, go back to training, check the game-plan, was it right not right, was the players I started with the right ones or not the right ones. But it's a lot of things to work around, but I got fix the individual mistakes so that the whole team can play."
Orlando Pirates sent a resounding statement in the Betway Premiership title race with a ruthless 6-0 demolition of TS Galaxy, as head coach Abdeslam Ouaddou hailed both the performance and mentality of his squad.
Pressure continues to mount at Magesi FC, but head coach Allan Freese has firmly pushed back against claims that he is to blame for the club's ongoing poor run of form.
It was a day of fine margins in the Betway Premiership as Golden Arrows, Siwelele and Durban City each secured hard-fought 1-0 victories, with late drama and decisive finishing proving the difference across three tightly contested encounters.
Orlando Pirates produced a dominant display with a Rele Mofokeng hat-trick boosting them to a 6-0 victory against ten-man TS Galaxy in the Betway Premiership clash at the Mbombela Stadium on Sunday.
