He made the announcement at a press conference on Tuesday as part of the Anglican Communion Primates' Meeting.
As soon as Welby imposes the consequences, SEC leaders will not be allowed to represent the Anglican Communion and cannot take part in any votes the Communion holds regarding doctrine or new rules.
Thirty-four of the 39 provinces in the Communion were represented by their archbishops. Welby said many archbishops expressed disappointment and anger over the issue but they were unanimously "satisfied" with the consequences the SEC will face.
The Archbishop of Canterbury said that he was personally "very sad" over the issue.
He said: "There were a lot of strong feelings [in the meeting].... but it was a bit different mood than many other Primates' meetings.
"It was more of a family that has to face the fact that something's happened that's causing grief, than a sort of club that doesn't like one of its members.
"The mood in the room... was grief that one has to do things that no one likes, that I don't particularly want to do. You want people to be united."
When asked to explain why the Church and General Synod changed its Canon on Marriage, Most Rev Mark Strange Primus of the Scottish Episcopal Church said it was a decision that was made with much prayer, theological debate and personal testimonies, but in the end the Church decided to allow those of different views to "walk together".
He added: "However, I recognise that this decision is one that has caused some hurt and anger in parts of the Anglican Communion and that the decision taken at the last Primates' Meeting, which was to exclude our brothers and sisters in The Episcopal Church from debate on Doctrine and from Chairing Anglican Communion Committees, is a decision that now also pertains to us.
"We will continue to play our part in the Anglican Communion we helped to establish, and I will do all I can to rebuild relationships, but that will be done from the position our Church has now reached in accordance with its synodical processes and in the belief that Love means Love."
Conservative Anglican Church group GAFCON said earlier on Tuesday that some of its Primates may walk out of the meeting if sanctions on the SEC don't call for repentance. There were no reports of Primates walking out on Tuesday.
The Archbishops of Nigeria, Rwanda and Uganda refused to attend this week's Anglican Primates' Meeting over what they deem as a weak stance on the issue of sexuality in the Church from the Communion.
