This has already been requested in https://pagure.io/pagure/issue/1628

The tldr is that pygit2 doesn't offer support for it (while libgit2 underneath does support it :(). In the mean while the PR page let you know if the merge is going to be a fast-forward or require a merge commit (I use this info to ask submitters to rebase their PR), or you can do the merge manually and adjust the commit message to contain a "Merges <url>" which will close the PR as merged when pushed (if you have the pagure hook enabled in the settings).

Closing as duplicate, but thanks for the report, it's always appreciated.