In Jira you can simply click on the placeholder image in the user profile (not in the administration screen), I think for confluence it should work the same.
You could also use the Confluence gravatar server so that it can be reused
https://marketplace.atlassian.com/plugins/net.vicox.confluence.plugins.gravatar
and as of 5.1 jira supports Gravatar
Another option is to do a SQL update on the databases. you can see the avatar setting with this query (in Jira)
select ID, filename, contenttype, avatartype, owner, systemavatar from jiradb
and your avatars are stored in the JIRA_HOME directory
\jira-home\data\avatars
I'm sure Confluence is pretty similar. You could do a bulk upload of images to the server and script SQL queries to do updates based on am input CSV data file. eg.
USER, AVATAR
abc, abcImg
def, defImg
ghi, ghiImg
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Use the JIRA SU & Confluence SU plugins to impersonate each user whose avatar you wish to change. For large instances, this may take some time :)
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