Aguero, making his first appearance for La Albiceleste since June 2016, tucked home debutant Cristian Pavon's cross at the second time of asking to earn his side a 1-0 victory at the Luzhniki Stadium.
Messi was playing just off the Manchester City striker and played a key part in the build-up to that late strike, but it was Aguero who received most of the plaudits after joining Hernan Crespo as Argentina's third all-time top scorer.
"This is what we are looking for. There was more vertical play with [Alejandro] Gomez next to [Angel] di Maria, interesting movements between Aguero and Messi, many movements on the wings," Sampaoli told reporters.
"[Aguero] read and understood the match very well in a few places. He had a couple of shots in the first half and another three in the second, one of which was a goal."
Messi will be absent for Argentina's friendly against Nigeria on Tuesday night, having been granted permission to return to club side Barcelona.