He encouraged the show of affection on the day Ms MacDonald's funeral took place in Edinburgh.
Mr Salmond, speaking at the SNP conference in Aberdeen, said the party had "many stars of Scottish politics" in its 80-year history.
"No star has burned more brightly and shone more luminously than Margo MacDonald," he said.
"I've been thinking about how best to recognise that contribution that Margo made to this party and this movement, and somehow a minute's silence isn't the Margo way.
"Let's give a resounding round of applause to the great contribution Margo MacDonald made to the SNP."
Ms MacDonald died at her home in Edinburgh last week after battling Parkinson's disease.
She had served as an SNP MP and MSP before becoming an independent politician at Holyrood, and had recently been attempting to change the law to allow assisted suicide.
Her funeral, at Mortonhall Crematorium, was attended by family and her closest friends.
Flags outside the Scottish Parliament flew at half-mast as a mark of respect.
A colourful celebration of her life will be held in Edinburgh on April 25.
The memorial ''is not to be an occasion for mourning'', according to her family, who are preparing a playlist of her favourite country music songs and have urged those attending to wear bright clothes.