Caballero doubled his tally for the night and made it 3-1 in the 53rd minute. Izwan failed to collect a cross from the edge of the box and Caballero swept it into an empty net.
In the 60th minute, Caballero thought he would be in for a hat-trick but his shot was well saved by Izwan.
Paraguay had another chance to add to their tally. Former Newcastle United midfielder Miguel Almiron, who had just come on, went close in the 74th minute, but he had his shot blocked by Ryhan Stewart.
Gomez and Enciso did come on, and the latter made it 4-1 in the 81st minute after being teed up by Almiron, smashing the ball past Izwan.
Enciso almost made it five in the 85th minute as his long-range shot thundered against the post, and Paraguay ran out comfortable winners.
Lee also said the team was aware of the issues it faced.
“We are very aware of the issues we have and we don’t want to hide behind it.
“We don’t want to be pointing fingers on anyone, but rather we should look at ourselves in the mirror first.”
Lee also stressed that such matches against high-quality opposition were valuable for the Lions.
“We want to be put under this kind of pressure. We want to be exposed like that,” said Lee.