The three-time African champions were outclassed in Bissau, just three days after opening their campaign with a 2-1 victory over Madagascar in Uyo.
Chelle admitted Guinea-Bissau were the better side but blamed the poor playing surface and hot weather for affecting his players.
“They were more aggressive than us, they were better than us,” Chelle’s told the media.
“Though this is not an excuse but they know their pitch, they usually play on this pitch but for us it was the first time and the pitch was very bad and the weather was very hot too.
“So Guinea-Bissau entered the game more motivated, more aggressive, they put more intensity and we never found a solution.”
Nigeria sit second in Group L with three points, three behind leaders Guinea-Bissau after two matches.