But the prospect of a fresh vote on leaving the UK - currently being considered by Nicola Sturgeon - came under fire from opposition MSPs who said it would lead to a fresh wave of austerity cuts.
Mr Mackay: "Small advanced economies around the world are doing better than Scotland.
"What's the one thing that we've got and they've not? That's independence.
"If we had the full levers of independence we would be able to stimulate our economy even further and have a more prosperous and fairer society."
The Finance Secretary said the the £13.4 billion deficit was only a "notional" figure and the product of the "current constitutional position, not Scottish independence."
But Tory finance spokesman Murdo Fraser said the GERS figures show the "reckless folly" of independence.
"What the GERS figures tell us is that the union dividend in Scotland in Scotland now amounts to £1,882 for every man woman and child which leads to record higher public spending per capita in Scotland of £1,576," Mr Fraser said.
"That's spending more than the UK average on schools and hospitals - on all the things that matter to us.
"It would be reckless folly to put these fiscal transfers from the rest of the UK at risk by pursuing a policy of Scottish separation."
Labour's James Kelly voiced fears about the impact of future austerity under independence if Scotland faced a £13.4 billion deficit.
"What areas of public spending would he propose to cut in his plan to try and sever the link of Scotland from the rest of the UK?" he asked Mr Mackay.