Bobby Zamora was on the bench for a game that kicked off at an earlier than scheduled 3.30pm. Phil Jagielka gave England the lead on 35 minutes, but hopes of securing the full three points were dashed when Stojkovski levelled after 65 minutes.
Meanwhile, reserve skipper Mark Hughes played for Northern Ireland under-21s in their 1-0 defeat to the Ukraine.
England Team: 1 Chris Kirkland, 2 Glen Johnson, 3 Paul Konchesky, 4 Joey Barton, 5 Phil Jagielka, 6 Peter Clarke, 7 Jermaine Pennant , 8 Steven Sidwell, 9 Francis Jeffers, 10 Shola Ameobi, 11 Michael Tonge. Subs: 12 Tony Hibbert, 13 Lee Grant, 14 Andrew Davies, 15 Gary O'Neil, 16 Shaun Wright-Phillips, 17 Jermain Defoe, 18 Bobby Zamora.
Paul Konchesky started for England under-21s in for the European Championship qualifier against Macedonia in Skopje - a game that finished 1-1.