The Warriors prevailed 16-15 for a ninth straight RaboDirect PRO12 win thanks to a Gordon Reid try and 11 points from fly-half Finn Russell.
Munster led thanks to Damien Varley's early try but the Warriors responded with three Russell penalties to lead 9-7 at the break.
Reid plunged over shortly after the break and while Sean Dougall went over for Munster's second try on 51 minutes, the visitors could not find the score they needed for victory.
The Warriors will now play the winner of Saturday's semi-final between Leinster and Ulster and should the latter win, Townsend's men would have home advantage.
"I'd like to play in Glasgow," said Townsend. "Leinster and Ulster are excellent sides and we've had battles with them both, just like we've had with Munster.
"I think that was one of the best games at this level that I've been involved in. It felt like Test-match intensity.
"Munster played outstanding rugby, they were very aggressive at the breakdown and moved the ball from minute one to minute 80.
"We had guys hobbling with cramp at the end with the effort they put in."
"Munster play a unique style, moving the ball wide to wide and, if you don't stick to your system, if you jump out line, then you'll get picked off.
"It's a lot of work to go up against that attack. But, if you get it right, you can put them under pressure and tackle them behind the gain line.
"We were almost there at times. We were getting real pace on the ball, but Munster defended really well."
Follow us on Facebook, join the conversation on Twitter, sign up to our YouTube channel for extensive match highlights and sign up for our newsletter for regular updates on the RaboDirect PRO12.
Guinness PRO12
Suite 208, Alexandra House,
The Sweepstakes
Ballsbridge, Dublin 4, Ireland