The Scots meet Belgium at Hampden Park on Friday and Macedonia in Skopje on Tuesday but did not include the Sunderland striker who has not started a match since damaging ankle ligaments on international duty in March.
McGhee wanted Fletcher in the squad but Strachan opted against it even though he only has Championship trio Jordan Rhodes (Blackburn Rovers), Ross McCormack (Leeds United) and Jamie Mackie (Nottingham Forest), League One striker Leigh Griffiths (Wolves) and Everton's Steven Naismith as forwards for the double header.
"I would like to think that were these two games critical to qualification that Steven Fletcher would have been on the phone to Gordon saying: 'I know I have only played half a game, but I want to come and be part of it'," said McGhee.
"The fact is that he will be bedding himself in a bit more carefully than that. We know how good a player he is and with the retirement of Kenny Miller he is even more important now. But we want the lad back fit and able to contribute from the front, rather than coming off the bench when he is only half fit.
"The manager was not tempted to bring him back, but I was. He ruled it out right away."