John Swinney praised Alex Salmond's "substantial and significant contribution" to Scottish and UK politics, as Holyrood remembered the former first minister.
A motion of condolence saw MSPs from all parties pay tribute to the Alba leader.
Mr Salmond died of a heart attack aged while attending a conference in North Macedonia just over two weeks ago.
A private funeral for friends and family took place in Strichen on Tuesday.
During the debate, the current First Minister acknowledged his relationship with Mr Salmond had "changed over the last six years".
He spent most of his allocated time reflecting on being finance secretary under Mr Salmond.
Mr Swinney said: “It was a relationship defined by the first minister wanting to spend more money than we actually had available… it was never a relationship without challenging moments but he did recognise, perhaps reluctantly, that possessing financial credibility was always an advantage in government.”
The Scottish Greens Co-leader Patrick Harvie said Mr Salmond “made a profound impact” on Scottish politics and said it was important to recognise his loss and offer “serious condolences”.
However, he added: “People’s lives and their legacies can be contested and they can be complicated so this is not a moment for an assessment of the entirety of the man. There will be more appropriate times for that.”
“The events of the last few years are an important part of his story but they do not change the fact that Alex Salmond was the political personality who enabled the SNP to advance in its political journey.”
Scottish Liberal Democrat leader Alex Cole-Hamilton agreed there would be a time to debate Salmond’s legacy "both personally and professionally" but today he said "it is important to reflect on his politics".
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Scottish Conservative leader Russell Findlay said it had been noted Mr Salmond was “a controversial and complicated” figure but today was not the day “for a verdict on his every action”.
He added Mr Salmond’s passing reminds everyone that life is “precious” and, using the words of Robert Burns whom Mr Salmond often quoted himself, the Scottish Conservative leader said, “nae man can tether time or tide”.
Scottish Labour leader Anas Sarwar agreed Mr Salmond was a “controversial but charismatic figure” and his loss has been “felt keenly” by the constituents he served when he was an MP at Westminster and an MSP at Holyrood.
Mr Sarwar recounted a time when Mr Salmond tried to convince his father, Mohammad Sarwar, a former Glasgow MP, that his son, the current Scottish Labour leader, should “ditch” his party and join the SNP.
Introducing the debate, Presiding Officer Alison Johnstone said parliaments and governments worldwide had messaged her about Mr Salmond’s passing and his “immense” political impact.
Mr Salmond led the SNP into power at Holyrood in 2007 and was at the helm of the party during the 2014 independence referendum.
When the Yes side lost with 45% of the vote, he stood down, famously telling reporters “the dream shall never die”.
Years after, Mr Salmond fell out with his successor Nicola Sturgeon over her government’s handling of harassment complaints against him.
He had the probe set aside with a judicial reviewing finding it had been “unlawful" and "tainted with apparent bias".
Ms Sturgeon did not take part in the debate.
In a statement, the former first minister said she had been “wrestling with how to pay appropriate respect to an individual who had a big impact on me”.
She said: “I have experienced a range of emotions since Alex Salmond’s death.
“I feel the loss of someone who for many years was an incredibly important person in my life. At the same time, I cannot pretend that the events of the past few years did not happen.
“At a very human level, I have been wrestling with how to pay appropriate respect to an individual who had a big impact on me – and on the life of the country – but in a way that feels right, and which does not distract from the grief of Alex’ family, who are the people who matter most right now.
“Weighing all this up, I have concluded that it is best for me to remember Alex privately. For the purposes of today that will mean watching the motion of condolence online rather than being physically present in the chamber.
“I appreciate that others in my position might make different decisions, but sometimes doing what feels most right is the best any of us can do.”
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