Ferguson, 31, and McGregor, 27, were sent home from training by Rangers and Ferguson was stripped of the club captaincy.
The Scottish FA said in a statement that the pair would no longer be considered for Scotland duty.
"Following on from the events of the past week - and specifically the last 48 hours - the Scottish FA has today confirmed that Barry Ferguson and Allan McGregor will no longer be considered for international selection by Scotland."
"This action has been taken in the best interests of the squad, the fans and the country," added the statement. "Everyone is determined to qualify for the World Cup and we must ensure that nothing is allowed to distract us from this goal."
Martin Bain, Rangers' chief executive, said on the Scottish Premier League club's website (www.rangers.co.uk) that the two players had been suspended after a drinking session and for also making V-sign gestures while sitting on the bench on Wednesday.
"The overall conduct of the players during the last week while on Scotland duty has, regrettably, fallen considerably short of the standards expected by Rangers Football Club and our supporters and has brought the club into disrepute," Bain added.
"The management of the club has taken the view that this has damaged both Rangers and Scotland and is unacceptable.
"Even though our club is entering the critical stage of the league season and the later stages of the Scottish Cup, appropriate disciplinary action was required."
"I apologise wholeheartedly for the embarrassment caused to Scotland, Rangers, both sets of supporters and my friends and family.
"I have always considered playing for Rangers and Scotland an honour and a privilege and nothing will change that and I am bitterly disappointed by the announcement that I will not be selected for Scotland again."
McGregor added: "I was absolutely delighted to be selected for Scotland last weekend and I am deeply sorry over what has happened s
