Dot has a special meaning in regular expressions - it matches anything (except for a newline). To match a dot literally, use [.] or \..

Also, use the /g modifier to replace all the occurrences on each line. 

s/\.\./,/g
# or
s/[.][.]/,/g

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لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: Replace ".." with "," by choroba
in thread [solved] Replace ".." with "," by zaqwsxcde

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