It may not be the best way, however it might be one way to split our string into three parts, maybe even before running it through RegEx engine. If that would not be the case and we wish to have an expression, this might be close:
(.+Encryption Algorithms:)|([a-z0-9-]+)(?:,|\s)|(MAC.+)

If you also have new lines, you might want to test with other expressions, maybe similar to:
([\s\S]+Encryption Algorithms:)|([a-z0-9-]+)(?:,|\s)|(MAC[\s\S]+)
([\w\W]+Encryption Algorithms:)|([a-z0-9-]+)(?:,|\s)|(MAC[\w\W]+)
([\d\D]+Encryption Algorithms:)|([a-z0-9-]+)(?:,|\s)|(MAC[\d\D]+)
RegEx
If this expression wasn't desired, it can be modified or changed in regex101.com.
RegEx Circuit
jex.im visualizes regular expressions:

Test
# coding=utf8
# the above tag defines encoding for this document and is for Python 2.x compatibility
import re
regex = r"([\w\W]+Encryption Algorithms:)|([a-z0-9-]+)(?:,|\s)|(MAC[[\w\W]+)"
test_str = ("SSH Enabled - version 2.0\n"
"Authentication methods:publickey,keyboard-interactive,password\n"
"Encryption Algorithms:aes128-ctr,aes192-ctr,aes256-ctr,aes128-cbc,3des-cbc,aes192-cbc,aes256-cbc\n"
"MAC Algorithms:hmac-sha1,hmac-sha1-96\n"
"Authentication timeout: 120 secs; Authentication retries: 3\n"
"Minimum expected Diffie Hellman key size : 1024 bits\n"
"IOS Keys in SECSH format(ssh-rsa, base64 encoded):\n")
subst = "\\2 "
# You can manually specify the number of replacements by changing the 4th argument
result = re.sub(regex, subst, test_str, 0, re.MULTILINE)
if result:
print (result)
# Note: for Python 2.7 compatibility, use ur"" to prefix the regex and u"" to prefix the test string and substitution.
Demo
const regex = /(.+Encryption Algorithms:)|([a-z0-9-]+)(?:,|\s)|(MAC.+)/gm;
const str = `SSH Enabled - version 2.0 Authentication methods:publickey,keyboard-interactive,password Encryption Algorithms:aes128-ctr,aes192-ctr,aes256-ctr,aes128-cbc,3des-cbc,aes192-cbc,aes256-cbc MAC Algorithms:hmac-sha1,hmac-sha1-96 Authentication timeout: 120 secs; Authentication retries: 3 Minimum expected Diffie Hellman key size : 1024 bits IOS Keys in SECSH format(ssh-rsa, base64 encoded):`;
const subst = `$2 `;
// The substituted value will be contained in the result variable
const result = str.replace(regex, subst);
console.log('Substitution result: ', result);