Pirates' 1-1 draw against Maritzburg United means they will not be able to finish in second place and secure a spot in next year's CAF Champions League after Mamelodi Sundowns beat SuperSrort United 2-1 in Tshwane.
MATCH REPORT: Maritzburg hold Buccaneers
The Buccaneers will now have to compete as far as they can in the CAF Confederation Cup, both this season and next, as far as their African ambitions go.
Moloi, who stepped in for media duties after caretaker coach Erick Tinkler was sent to the stands at Harry Gwala Stadium, is not worried about a hectic upcoming fixture schedule should Bucs beat AS Kaloum of Guinea and reach the Confederation Cup group stages.
"It's all about periodisation and regenerating the players for the next game," Moloi explained.
"The players have been through what we're going through now, and they understand the importance of each and every game both in the PSL and CAF and they are coping very well.
"You can see there's a lot of rotation in the team; players like Menzi Masuku who was not registered for CAF, today they got their chance and in the previous game they came on and did very well for us.
"We have a balanced squad and we've struck a balance very well."
On the Maritzburg game, he added: "Difficult game, Maritzburg always gives us a hard time, even the last time we played them we lost two zero at FNB.
"We all know Steve [Komphela] is a very tactical coach, he will always try to unsettle our players and you look at the way they were physical and broke down our attacks, the guys gave it their best shot."
Goalscorer Kermit Erasmus, who netted his 15th goal in all competitions on Wednesday night, was disappointed to see second place slip away.
"It's very disappointing," he added. "We wanted to finish second to qualify for the Champions League, we came for the three points but it's part of the game."