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(1).replace(',', ':'), line))
aW1wb3J0IHJlCmxpbmUgPSAnMTIvMDgvMjAxMywzLCI5LDI1Iiw0Mjo1MSwiMywwOCIsIjEyLDkiLCIxMyw5IiwxNTksMTcwLCIzLDE5Iiw0MzcsJwpwcmludChyZS5zdWIociciKFteIl0qKSInLCBsYW1iZGEgeDogeC5ncm91cCgxKS5yZXBsYWNlKCcsJywgJzonKSwgbGluZSkp
12/08/2013,3,9:25,42:51,3:08,12:9,13:9,159,170,3:19,437,