The party's conduct committee met on Thursday to discuss his case after he refused to immediately rejoin the group.
MacNeil was suspended from the party's Westminster group last month after reportedly clashing with chief whip Brendan O'Hara.
He tweeted about his expulsion, using a kangaroo emoji to refer to the member conduct committee. He said: "The Summer of Member Expulsion, has indeed come to pass. As I have been expelled as a rank & file SNP member by a 'member conduct committee'. He was suspended from the Westminster group for a week in early July following reports of a row with Mr O'Hara in the House of Commons. Later that month his membership of the party was suspended as he refused to immediately rejoin the SNP group.
Thursday's decision by the conduct committee means he cannot sit as an SNP MP any longer and appears to rule out any reconciliation with the party. On Wednesday, SNP Westminster leader Stephen Flynn was asked about Mr MacNeil as he spoke to journalists on the by-election campaign trail in Rutherglen and Hamilton West.
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