McNamara sacrificed what could have been his first cup final as a manager when he left Firhill for Tannadice in January with Thistle in the Ramsdens Cup final against Queen of the South.
But he is potentially 90 minutes away from leading a second club to a cup final in the same season after Gary Mackay-Steven scored a 35th-minute winner in the Dens Park quarter-final.
McNamara said: "It's great. I'm delighted for the fans and everyone connected with the club.
"I left Thistle in a final of the Ramsdens Cup and hopefully we can get to the final of the Scottish Cup and make up for that."
McNamara added: "We can play a lot better and can pass the ball better, but credit to Dundee - they made it hard for us.
"John will be happy with the spirit of his team and I'm delighted with the spirit of my team and the commitment."