The Jags lost their perfect record at Firhill this season in frustrating fashion as Andy Barrowman headed home in the first half to book Dunfermline's place in today's last-16 draw.
The goal came just moments after defender Aaron Muirhead saw red for a last-man challenge on former Jags striker Craig Dargo, with a second-period onslaught from McNamara's men not enough to snatch a replay.
Thistle did have their chances, most notably a Ross Forbes penalty that was touched on to the post by visiting keeper Paul Gallacher before eventually being cleared, but the afternoon was to end in frustration for the Irn-Bru First Division leaders over their rivals, who are in second on goal difference.
McNamara said: "I thought we would get chances in the match, which we did.
"We knew towards the end that they would have a few breakaways as we pushed forward.
"But I am very proud of my players and the way they kept battling, even with 10 men, for such a long, long period of the match.
"I think we contributed to what was a good cup tie. It just wasn't going to be our day with the penalty save and Gallacher has had another couple of good saves as well.
"I can't ask for any more from the players. But we are of course disappointed to be out the cup.
"I still felt confident that we were going to get a goal. Even going into injury-time I still believed we were going to get something from the match.
"The players are gutted because they put so much effort into the match. A few things went against us but that happens.
"You could say that we can now concentrate on the league, but I am disappointed because we wanted to get a good run in the cup.
"The way it panned out with the sending off and the way we lost the game, sometimes that happens in football. But I am very proud of the lads and the way they went about it."
Having recorded two wins over Jim Jefferies' side already this season, including a 5-1 league rout last month, Thistle went into the cup clash in high spirits as they looked to inflict another defeat on their title rivals.
But Muirhead's red on the half-hour mark proved decisive as the Pars saw the game out, with Barrowman also seeing red for two rash challenges late on in the match.
McNamara, who must now try and lift his side for a trip to Cowdenbeath on Saturday, said: "Wee things can change the game and the sending off was a big thing for us.
"I am disappointed because it has come from our goal kick. Dargs has used his experience and it was a big change in the match.
"I will have to see it again. Whether or not he is offside when they first won the header, I don't know.
"Aaron Muirhead is the wrong side of him, I don't know how much contact was there but Dargs seemed to think there was a lot.
"He is experienced and I think that was the telling factor."