Ex-Wolves boss McCarthy handed Doherty a start at left-back for the 0-0 draw with Georgia on Friday.
But the right wing-back moved to the bench for the 2-0 defeat over the Swiss as Sheffield United's Enda Stevens returned from suspension.
He did not make it on to the pitch on Wednesday night, but with Everton wing-back Seamus Coleman picking up a red card and one-match ban, Doherty is expected to return to the starting XI for the crunch clash with Denmark on November 18.
The Republic are still top of the Group D table with 12 points, but are level on points with the Danes and just a point above the Swiss going into that final game.
Denmark and Switzerland have a game in hand on McCarthy's men with all three battling it out for the two qualification spots.
But McCarthy backed Doherty to fill the void left by Coleman as he already focuses on that November 'cup final' at their Dublin Aviva base.
He said: "Matt is in the box seat now to be playing. He's a Premier League footballer so there's no issues there.
"To get first or second (in the group) was always going to be an over-achievement I think when you look at the two teams.
"(But) we've still got a chance to do it.
"(We have) a cup final in the Aviva on November, 18.
"I'd have taken that before and I'll take it now."