import re
line = '12/08/2013,3,"9,25",42:51,"3,08","12,9","13,9",159,170,"3,19",437,'
print(re.sub(r'"[^"]*"', lambda x: x.group(0).replace(',', ':'), line))
aW1wb3J0IHJlCmxpbmUgPSAnMTIvMDgvMjAxMywzLCI5LDI1Iiw0Mjo1MSwiMywwOCIsIjEyLDkiLCIxMyw5IiwxNTksMTcwLCIzLDE5Iiw0MzcsJwpwcmludChyZS5zdWIociciW14iXSoiJywgbGFtYmRhIHg6IHguZ3JvdXAoMCkucmVwbGFjZSgnLCcsICc6JyksIGxpbmUpKQ==
12/08/2013,3,"9:25",42:51,"3:08","12:9","13:9",159,170,"3:19",437,