The Liverpool defender played the 90 minutes for his country in Ljubljana as they looked to secure the victory needed to seal a place in the play-off round for next year’s tournament.
However, after a bright start in which Leigh Griffiths gave Scotland the lead just after the half-hour mark, the hosts struck back after the interval via a Roman Bezjak brace to go 2-1 in front.
Robert Snodgrass did equalise in the 88th minute, but the stalemate means they finish third in Group F and miss out due to an inferior goal difference to Slovenia.
Elsewhere, Jordan Henderson completed the game and Daniel Sturridge came on in the 72nd minute as England beat Lithuania 1-0 in their final qualifier, with a place in the World Cup finals already assured prior to kick off.
Alex Oxlade-Chamberlain was an unused substitute for the Three Lions in Vilniaus.
Meanwhile in Germany, Can netted his first goal for his country in a 5-1 win over Azerbaijan.
The Reds' No.23 rounded off the scoring at the Fritz-Walter-Stadion with a thumping 25-yard drive on 81 minutes.