diff --git a/jax/_src/pjit.py b/jax/_src/pjit.py
index a5631573707b..a3eeb61f1403 100644
--- a/jax/_src/pjit.py
+++ b/jax/_src/pjit.py
@@ -76,7 +76,7 @@
 from jax._src.util import (
     HashableFunction, safe_map, safe_zip, wraps,
     distributed_debug_log, split_list, weakref_lru_cache,
-    merge_lists, flatten, unflatten, subs_list2)
+    merge_lists, flatten, unflatten, subs_list)
 
 map, unsafe_map = safe_map, map
 zip, unsafe_zip = safe_zip, zip
@@ -1798,8 +1798,8 @@ def _pjit_partial_eval(trace, *in_tracers,
 
   known_ins = tuple(pv.is_known() for pv in in_pvals)
   unknown_ins = tuple(not k for k in known_ins)
-  known_jaxpr, unknown_jaxpr, unknown_outs, res_avals = pe.partial_eval_jaxpr_nounits(
-      jaxpr, unknown_ins, instantiate=False)
+  known_jaxpr, unknown_jaxpr, unknown_outs, res_avals = \
+      pe.partial_eval_jaxpr_nounits(jaxpr, unknown_ins, instantiate=False)
   unknown_outs = tuple(unknown_outs)
   known_outs = tuple(not uk for uk in unknown_outs)
   num_residuals = len(res_avals)
@@ -1808,28 +1808,34 @@ def _pjit_partial_eval(trace, *in_tracers,
   def keep_where(l, should_keep):
     return tuple(x for x, keep in zip(l, should_keep) if keep)
 
-  # Compute which outputs are just forwarded inputs.
+  # Input-to-output forwarding: compute which outputs are just forwarded inputs.
   num_out_primals = len(known_jaxpr.out_avals) - num_residuals
-  in_fwd = pe._jaxpr_forwarding(known_jaxpr.jaxpr)
-
+  in_fwd: list[int | None] = pe._jaxpr_forwarding(known_jaxpr.jaxpr)
   # Only forward primal outputs when corresponding out_sharding is UNSPECIFIED.
   in_fwd_primal, in_fwd_res = split_list(in_fwd, [num_out_primals])
   in_fwd = [fwd if is_unspecified(os) else None for os, fwd in
             zip(keep_where(out_shardings, known_outs), in_fwd_primal)
             ] + in_fwd_res
   del in_fwd_primal, in_fwd_res
+  # Prune jaxpr outputs and out_shardings by removing the input-forwards.
+  keep = [f is None for f in in_fwd]
+  known_jaxpr = pe.prune_closed_jaxpr_outputs(known_jaxpr, keep)
+  known_out_shardings = keep_where(out_shardings, known_outs) + res_shardings
+  known_out_shardings = keep_where(known_out_shardings, keep)
+  # Update num_out_primals to reflect pruning.
+  kept_primals, kept_res = split_list(keep, [num_out_primals])
+  num_out_primals = sum(f is None for f in kept_primals)
+  del keep, kept_primals, kept_res
 
-  # Compute which residuals are just primal outputs.
+  # Output-to-output forwarding: compute which residuals are just primal outputs
   out_vars, res_vars = split_list(known_jaxpr.jaxpr.outvars, [num_out_primals])
   idx_map = {id(v): i for i, v in enumerate(out_vars)}
   out_fwd = [None] * num_out_primals + [idx_map.get(id(v)) for v in res_vars]
-
-  # Prune jaxpr outputs and out_shardings by removing forwards.
-  keep = [f1 is None and f2 is None for f1, f2 in zip(in_fwd, out_fwd)]
+  # Prune jaxpr outputs and out_shardings by removing forwarded residuals.
+  keep = [f is None for f in out_fwd]
   known_jaxpr = pe.prune_closed_jaxpr_outputs(known_jaxpr, keep)
-  known_out_shardings = keep_where(out_shardings, known_outs) + res_shardings
   known_out_shardings = keep_where(known_out_shardings, keep)
-  del keep, num_out_primals
+  del keep
 
   known_params = dict(
       jaxpr=known_jaxpr, in_shardings=keep_where(in_shardings, known_ins),
@@ -1841,16 +1847,18 @@ def keep_where(l, should_keep):
   # Bind known things to pjit_p.
   known_inputs = [pv.get_known() for pv in in_pvals if pv.is_known()]
   all_known_outs = pjit_p.bind(*known_inputs, **known_params)
-  all_known_outs = subs_list2(in_fwd, out_fwd, known_inputs, all_known_outs,
-                              all_known_outs)
+  # Add back in the output fwds.
+  all_known_outs = subs_list(out_fwd, all_known_outs, all_known_outs)
+  # Add back in the input fwds.
+  all_known_outs = subs_list(in_fwd, known_inputs, all_known_outs)
 
   known_out_vals, residual_vals = \
       split_list(all_known_outs, [len(all_known_outs) - num_residuals])
   residual_tracers = map(trace.new_instantiated_const, residual_vals)
 
-  # The convention of partial_eval_jaxpr_nounits is to place residual binders
-  # at the front of the jaxpr produced, so we move them to the back since both
-  # the jaxpr equation built below and the pjit transpose rule assume a
+  # The convention of partial_eval_jaxpr_nounits is to place residual binders at
+  # the front of the jaxpr produced, so we move them to the back since both the
+  # jaxpr equation built below and the pjit transpose rule assume a
   # residual-inputs-last convention.
   unknown_jaxpr = pe.move_binders_to_back(
       unknown_jaxpr, [True] * num_residuals + [False] * sum(unknown_ins))