In the 13th minute of the match played in Hanoi, Toan received the first yellow when he attempted to prevent a counterattack and fouled Malaysia's Darren Lok.
Japanese referee Ryuji Sato then flashed the second in the 32nd minute when Toan tripped Dominic Tan to again stop a counterattack, and was sent off leaving Vietnam to play with 10 men.
Speaking after the game, Duc said: "I don't think Van Toan deserved a second yellow card."
Several experts concurred with him, saying most referees would not have given Toan a second yellow resulting in his send-off since the foul was not serious and would have merely "warned" him.
Vietnamese coach Park Hang-seo said Toan did not intentionally foul the Malaysian player.
Despite playing with 10 men, Vietnam won 3-0 to go to the top of group B.