Git over ssh and http are different things.

config/gitlab.yml.example

@@ -203,8 +203,8 @@ production: &base
   git:
     bin_path: /usr/bin/git
     # Max size of a git object (e.g. a commit), in bytes
-    # This value can be increased if you have very large commits
-    # Please also change the limit for your webserver (for Nginx see lib/support/nginx/gitlab)
+    # This value can be increased if you have very large commits with git over ssh
+    # Git over http is limited by your webserver (for Nginx see lib/support/nginx/gitlab)
     max_size: 5242880 # 5.megabytes
     # Git timeout to read a commit, in seconds
     timeout: 10

lib/support/nginx/gitlab

@@ -12,8 +12,8 @@ server {
   server_tokens off;     # don't show the version number, a security best practice
   root /home/git/gitlab/public;
   
-  # Set value of client_max_body_size to at least the value of git.max_size in gitlab.yml
-  # Also increase this if you want to upload large attachments
+  # Increase this if you want to upload large attachments
+  # Or if you want to accept large git objects over http
   client_max_body_size 5m;
 
   # individual nginx logs for this gitlab vhost