Scotland's Deputy First Minister was speaking following an announcement from Nicola Sturgeon at her Covid briefing on Tuesday that all sporting events in Scotland will be restricted to 500 spectators for a period of three weeks, from and including Boxing Day, in a bid to help reduce the spread of Omicron.
The new restrictions come just days after 50,000 spectators gathered at Hampden to witness Celtic lift the first silverware of the Scottish football season with a 2-1 win over Hibs at the national stadium in Glasgow.
Thousands of fans travelled to the match in trains, buses and cars and Swinney admitted that it could have contributed to a spike in Covid cases.
Speaking to BBC Radio Scotland, Swinney said: "It stands to reason that if we have 50,000 fans travelling towards a sporting event in one particular part of the country, using multiple modes of transport and interacting with each other there is a very high danger that will be a super-spreader event.
"[The cup final] could well be [a super-spreader], and I regret the fact we didn't make this decision earlier. That's nobodies fault. I was one of the people involved in the decision. I didn't take the decision earlier, so I'm part of that decision-making process.
"But I have to acknowledge that events of that nature have the potential to be super spreader events, and the government if it's acting in the interest of the public health of our community, has got to take some difficult decisions that people will not like, but are designed to act in the public interest."
Swinney also responded to a statement from Celtic requesting that all Scottish Premiership fixtures are postponed over the period that the restrictions apply to, which would include the Old Firm match against Rangers at Parkhead scheduled for January 2.
"I think that's a very good idea," he said.
"I welcome the intervention of Celtic FC and I see that some other football voices have been saying much the same point.
"I think that is welcome. It recognises the contribution that all of us have got to make to try to deal with the situation we face.
"I fully appreciate the frustration and the irritation that football fans will feel about this.
"I dont take part in these decisions lightly at all, but I think they are necessary to protect the public.
"But I think the suggestion from Celtic FC is a welcome suggestion."