The Manchester United striker was sent off after lashing out at Miodrag Dzudovic with England leading 2-1.
Andrija Delibasic grabbed a late leveller for the hosts, guaranteeing Montenegro a play-off spot but also securing England the point they needed to creep over the line as group winners.
Ashley Young and Darren Bent's goals put England in command in the first half but Elsad Zverotic's goal on the stroke of half-time saw the tide begin to turn, and now England face being without star striker Rooney for at least the first group game in Poland and Ukraine.
Terry told Sky Sports: "He had a little bit of a tussle and it's one of those things. Fortunately we're through and it didn't cost us so we're happy that we're through and that goes for everyone.
"Tonight was always going to be tough, Switzerland away was going to be tough, so all over the campaign we can be pleased with how we've come on since the World Cup.
"We're a little bit disappointed obviously after being 2-0 up, we're disappointed to end up drawing the game. But it's a great thing to get where we've got, we're top and we've worked hard all the way through."