The stoppage-time drama saw Carvalhal get involved with a steward before being ordered down the tunnel by referee David Webb.
A statement on the FA website reads: "Carlos Carvalhal will serve a two-match touchline ban with immediate effect following an Independent Regulatory Commission hearing on Thursday [7 September 2017].
"The Sheffield Wednesday manager was charged for misconduct in relation to his behaviour in the 88th minute of the EFL Cup game against Bolton Wanderers on 22 August 2017.
"The charge was designated as a non-standard case as this was Mr Carvalhal’s second misconduct charge within 12 months.
"Mr Carvalhal, who partially admitted the charge and requested a personal hearing, was also fined £4000. Bolton manager Phil Parkinson was fined £2000 after admitting misconduct during the same fixture and accepted the standard penalty."
Sheffield's sports scientist Andy Kalinins, who was also charged for misconduct, has been banned as well and is poised to pay a £3000 fine.