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Mr MacNeil, the MP for Na h-Eileanan an Iar - or the Western Isles - was suspended from the party's group in Westminster last month after a reported clash with Brendan O'Hara.
An investigation then took place into the MP's decision not to rejoin the party's Westminster group following his suspension, which lasted a week.
Mr MacNeil previously said his decision not to rejoin the group was not linked to that incident, and instead criticised the SNP over its independence strategy.
He said at the time that he would only rejoin following the party's conference in October if it "is clear that the SNP are pursuing independence".
The party's conduct committee then met this Thursday to discuss his case.
In a tweet about his expulsion, Mr MacNeil used a kangaroo emoji to refer to the conduct committee that made the decision.
"I didn't leave the SNP - the SNP have left me. I wish they were as bothered about independence as they are about me!" he wrote.
The decision means Mr MacNeil will sit as an independent MP in the Commons, of which there are now 15 in total.
On Wednesday, SNP Westminster leader Stephen Flynn was asked about Mr MacNeil on the by-election campaign trail in Rutherglen and Hamilton West, the seat made vacant following the successful recall petition against Margaret Ferrier.
He told reporters the party's MPs should not "pick and choose" when they hold the party whip.
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However, he said he would not give a "running commentary" on the conduct process and he "gets on well with Angus".
Mr Flynn said he and his colleagues wanted a "positive outcome" but added this was not always possible in politics.
Since his expulsion, Mr MacNeil has been posting critical tweets on social media about the SNP's power-sharing deal with the Green Party, also known as the Bute House agreement.
"Only dogged la-la-land thinking keeps this daft and dangerous agreement going," he said.