“Should I bring on Kun [Aguero]?” Sampaoli asked Messi during the game, according to the Argentine sports daily Ole.
Aguero came on from the bench in the 80th minute of the match, which the South Americans eventually won 2-1 thanks to a late goal by Marcos Rojo.
Argentina scraped into the knockout stage after Croatia beat Iceland by the same scoreline in the other Group D match on Tuesday.
Earlier, media reported that the Argentina players had unanimously voted for Sampaoli to be sacked, following the team’s lacklustre performance in their opening two World Cup games, and would have a say in who should play against Nigeria.
Argentina will next face Group C winners France in their round of 16 matches, which will be played in Kazan on Saturday.