Salmond said the Health Secretary had a "different recollection" amid claims Yousaf deliberately set up a diary clash to miss the vote.
Gay marriage has been a key issue in the contest, with candidate Kate Forbes saying she would have voted against it.
Yousaf is also under scrutiny as he missed the final vote after arranging a meeting with the Pakistani government.
Former MSP Alex Neil said Yousaf intentionally missed the vote and Salmond, who leads Alba, has also entered the row.
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