The striker had helped set up both England goals before being sent off for a kick at Miodrag Dzudovic with 20 minutes left, putting his side under pressure.
England went on to concede a late equaliser but hung on for the point they needed to top Group G.
Newspapers took a swipe at the striker.
"We will Roo this moment", "Roo Fool!" and "An Idiot Abroad" read some of the headlines.
As the game was England's last qualifier, he faces a minimum one-match ban for June's finals in Ukraine and Poland but that could be increased by UEFA.
England have no other player like Rooney, who can be deadly as a striker but also link up play.
Coach Fabio Capello defended his decision to pick Rooney, who was also sent off in the 2006 World Cup, after the player's father and uncle were arrested on Thursday and bailed by police over an alleged betting scam.
"It was no mistake to pick him. I spoke with him before the game and he was relaxed and calm, then went out on the pitch and made this silly mistake," the Italian told reporters.
Captain John Terry tried to look on the bright side.
"We can look over the course of this campaign and be pleased at how we've come back after the [2010] World Cup," he said.
"We've seen players come in and refresh the group, playing for places. There have been a lot of young players coming in and with the established players we have as well, we've always said it's a great mix."
Montenegro coach Branko Brnovic was thrilled that the tiny Adriatic republic, whose population is only 650,000, secured second spot and a playoff berth thanks to the draw.
Asked about Rooney, he told reporters: "When I read about his family problems I thought he wouldn't play at all, so it's hardly surprising he got himself sent off because no one would find it easy in a situation like his."
It was the first game in charge for Brnovic, who stepped in for Zlatko Kranjcar last month after the Croatian was sacked following a 2-1 defeat in Wales.
"I have to thank Kranjcar for what he did while he was in charge and [Montenegrin Football Association President] Dejan Savicevic. They both deserve credit for getting Montenegro into a position to achieve this historic success," he said.
Montenegro first played as an independent nation after splitting from Serbia in the World Cup 2010 qualifiers when they registered one win in 10 games.
