diff -ru a/tools/build/src/tools/python.jam b/tools/build/src/tools/python.jam
--- a/tools/build/src/tools/python.jam
+++ b/tools/build/src/tools/python.jam
@@ -746,7 +746,7 @@ local rule configure ( version ? : cmd-or-prefix ? : includes * : libraries ? :
     {
         # Values to be extracted from python's sys module. These will be set by
         # the probe rule, above, using Jam's dynamic scoping.
-        local sys-elements = version platform prefix exec_prefix executable ;
+        local sys-elements = version platform base_prefix base_exec_prefix executable ;
         local sys.$(sys-elements) ;

         # Compute the string Python's sys.platform needs to match. If not
@@ -786,10 +786,10 @@ local rule configure ( version ? : cmd-or-prefix ? : includes * : libraries ? :
                 {
                     debug-message ...requested configuration matched! ;
 
-                    exec-prefix = $(sys.exec_prefix) ;
+                    exec-prefix = $(sys.base_exec_prefix) ;
 
                     compute-default-paths $(target-os) : $(sys.version) :
-                        $(sys.prefix) : $(sys.exec_prefix) ;
+                        $(sys.base_prefix) : $(sys.base_exec_prefix) ;
 
                     version = $(sys.version) ;
                     interpreter-cmd ?= $(cmd) ;
