In a gritty promotion/relegation play-off tie, Asanda Mvalo and Edwin Sitaytayi eclipsed Nasief Morris's first-half opener at Athlone Stadium.
The result leaves the People's Team and Amabhubesi on four points - two more than Chippa United, who have a game in hand.
"First half we played well, we put ourselves in the position which we wanted with the one zero score," Nooij told the Premier Soccer League's official website.
"Second half we came out to finish it, to look for the second goal, which was very possible in the first 10 minutes when we had three good opportunities.
"But then, like what always seems to happen in football, the opponent came out and scored from an unexpected corner. Two headers in our own box beat us.
"They basically had three opportunities and they scored two, we had more than five chances and scored only one goal.
"The nasty thing for us is if you look at how the team played, they did well, but when we made some substitutions suddenly we were giving the ball to the opponent.
"Unfortunately Santos is still strong at complicating our own affairs when we are in a comfortable position," concluded the Dutchman.