In this usage, they are synonymous, but 'least' is perhaps more appropriately mathematical vocabulary. 'Least' of course has other uses, as does 'lowest':
'That is the least of my worries.' 'He is at the lowest step of the ladder of success.'
"Lowest" is correct because it is the superlative of "low," which can be used to describe "number," whereas "least" is more often used to describe adjectives and adverbs. "Least" is the superlative of "less," which cannot be used to describe "number."
OK: low number, lower number, lowest number (and the related: high number, higher number, highest number) NOT OK: less number, least nu