diff --git a/Library/Homebrew/formula_auditor.rb b/Library/Homebrew/formula_auditor.rb
index bb6507fefa..a08bb73d26 100644
--- a/Library/Homebrew/formula_auditor.rb
+++ b/Library/Homebrew/formula_auditor.rb
@@ -344,6 +344,10 @@ module Homebrew
       recursive_runtime_formulae.each do |f|
         name = f.name
         unversioned_name, = name.split("@")
+        # Allow use of the full versioned name (e.g. `python@3.99`) or an unversioned alias (`python`).
+        next if formula.tap&.audit_exception :versioned_formula_dependent_conflicts_allowlist, name
+        next if formula.tap&.audit_exception :versioned_formula_dependent_conflicts_allowlist, unversioned_name
+
         version_hash[unversioned_name] ||= Set.new
         version_hash[unversioned_name] << name
         next if version_hash[unversioned_name].length < 2
diff --git a/Library/Homebrew/tap_auditor.rb b/Library/Homebrew/tap_auditor.rb
index d946a12e27..16bd6e1444 100644
--- a/Library/Homebrew/tap_auditor.rb
+++ b/Library/Homebrew/tap_auditor.rb
@@ -8,8 +8,8 @@ module Homebrew
   class TapAuditor
     extend T::Sig
 
-    attr_reader :name, :path, :formula_names, :cask_tokens, :tap_audit_exceptions, :tap_style_exceptions,
-                :tap_pypi_formula_mappings, :problems
+    attr_reader :name, :path, :formula_names, :formula_aliases, :cask_tokens,
+                :tap_audit_exceptions, :tap_style_exceptions, :tap_pypi_formula_mappings, :problems
 
     sig { params(tap: Tap, strict: T.nilable(T::Boolean)).void }
     def initialize(tap, strict:)
@@ -21,6 +21,7 @@ module Homebrew
       @tap_pypi_formula_mappings = tap.pypi_formula_mappings
       @problems                  = []
 
+      @formula_aliases = tap.aliases
       @formula_names = tap.formula_names.map do |formula_name|
         formula_name.split("/").last
       end
@@ -68,7 +69,9 @@ module Homebrew
 
       list = list.keys if list.is_a? Hash
       invalid_formulae_casks = list.select do |formula_or_cask_name|
-        @formula_names.exclude?(formula_or_cask_name) && @cask_tokens.exclude?("#{@name}/#{formula_or_cask_name}")
+        formula_names.exclude?(formula_or_cask_name) &&
+          formula_aliases.exclude?(formula_or_cask_name) &&
+          cask_tokens.exclude?("#{@name}/#{formula_or_cask_name}")
       end
 
       return if invalid_formulae_casks.empty?