The Bolton defender rued the the Manchester United striker's sending off but was full of praise for the performance of Phil Jones, who made his international debut in Podgorica
The former Everton star was shown a straight red card for kicking out at Miodrag Dzudovic during the second half and although the Three Lions surrendered a two-goal lead to draw 2-2, the result was enough to book their place in Poland and Ukraine as group winners.
Despite Rooney's red card souring England's qualification, Cahill hailed the achievement of reaching next summer's finals although admitted that it will be a "big blow" to be without the 25-year-old for the start of the tournament.
"It will be a massive blow with the talent Wayne has," Cahill said. "He is phenomenal. It is going to be a big blow at the finals.
"Going down to 10 men was tough but the main thing was we got the job done in difficult circumstances.
"When something like that happens, you've got to deal with it and carry on and that's what we did.
"I hope everyone sees it as a job done. We've done terrifically well to get to the tournament and we are looking forward to it now."
The Bolton defender also praised the performance of Manchester United defender Phil Jones, who made his international debut for Fabio Capello's side in Montenegro.
"I thought Phil did really well, he got forward when he could, he defended well in really difficult circumstances," Cahill added.
"It was a hard game for him to get his first cap. It was a big game and conditions didn't help him.
"But he has already looked at home with Manchester United this season since moving there.
"He did really well in Montenegro. He really stood up to the task and seeing youngsters coming through and doing well is great for England.
"I think we are in really good shape. We've got young players coming through now with a blend of experience as well.
"That will stand us in good stead for the tournament and a couple more games before we get there. I think we will do really well."