England embarrassingly appealed for offside, but Wayne Bridge and, ludicrously, Shaun Wright-Phillips - who should not have been that far back - were both clearly playing him on.
The tireless Wayne Rooney flashed a shot wide before Wright-Phillips volleyed home the second in the 75th minute after another replacement James Milner saw his first time effort parried out by Essam El Hadary.
Wayne Rooney, subdued for the most part, shot just wide, while substitute Shaun Wright-Phillips, on for the under-par Milner after only 30 minutes, saw his angled drive saved by Howard.