It's a BUG!

You are right that in Perl, 'A=1,B=2,C=3,' =~ /.*B=.*?,/; print $& prints A=1,B=2,

What you have stumbled upon is a bug that still exists in Oracle Database 11g R2. If the exact same regular expression operator (excluding the greediness modifier) appears twice in a regular expression, both occurrences will have the greediness indicated by the first appearance regardless of the greediness specified by the second one. That this is a bug is clearly demonstrated by these results:

SQL> SELECT regexp_substr('A=1,B=2,C=3,', '[^B]*B=[^Bx]*?,') as good FROM dual;

GOOD
--------
A=1,B=2,

SQL> SELECT regexp_substr('A=1,B=2,C=3,', '[^B]*B=[^B]*?,') as bad FROM dual;

BAD
-----------
A=1,B=2,C=3,

The only difference between the two regular expressions is that the "good" one excludes 'x' as a possible match in the second matching list. Since 'x' does not appear in the target string, excluding it should make no difference, but as you can see, removing the 'x' makes a big difference. That has to be a bug.

Here are some more examples from Oracle 11.2: (SQL Fiddle with even more examples)

SELECT regexp_substr('A=1,B=2,C=3,', '.*B=.*?,')  FROM dual; =>  A=1,B=2,C=3,
SELECT regexp_substr('A=1,B=2,C=3,', '.*B=.*,')   FROM dual; =>  A=1,B=2,C=3,
SELECT regexp_substr('A=1,B=2,C=3,', '.*?B=.*?,') FROM dual; =>  A=1,B=2,
SELECT regexp_substr('A=1,B=2,C=3,', '.*?B=.*,')  FROM dual; =>  A=1,B=2,
-- Changing second operator from * to +
SELECT regexp_substr('A=1,B=2,C=3,', '.*B=.+?,')  FROM dual; =>  A=1,B=2,
SELECT regexp_substr('A=1,B=2,C=3,', '.*B=.+,')   FROM dual; =>  A=1,B=2,C=3,
SELECT regexp_substr('A=1,B=2,C=3,', '.+B=.+,')   FROM dual; =>  A=1,B=2,C=3,
SELECT regexp_substr('A=1,B=2,C=3,', '.+?B=.+,')  FROM dual; =>  A=1,B=2,

The pattern is consistent: the greediness of the first occurrence is used for the second occurrence whether it should be or not.