Victory over Ottmar Hitzfeld's well-organised but beatable Swiss side would have kept up England's momentum after winning three of their opening four Group G matches although they do remain top with 11 points from five games.
Montenegro, who started the day in second place with 10 points from four matches, were on course to replace England as group leaders but were held to a 1-1 by Bulgaria in Podgorica.
Switzerland, a distant third in the group, took control with Tranquillo Barnetta scoring direct from free-kicks after 32 and 35 minutes following poor defending by England.
The hosts struck back when Frank Lampard converted a 37th-minute penalty and equalised six minutes into the second half when Ashley Young, who replaced the Chelsea midfielder at half-time, scored with a first-time shot.
Striker Darren Bent then missed an easy chance for England after 71 minutes when he skied the ball over the bar with Swiss goalkeeper Diego Benaglio on the ground - one of four good opportunities the home team squandered after pulling level.
England coach Fabio Capello, who surprisingly left Young on the bench at the start, was disappointed with the result and said he brought the winger on at half-time to inject some pace.
"At 2-0 down I was hoping to recover the result but after we got back to 2-2 we had four good chances to score," Italian Capello told reporters.
"Some of my players had no energy left in the last 10 minutes and you need that because the Swiss have some very good quality players and in modern football if you can't press it's difficult."
TURNING POINT
Hitzfeld said England's first goal, coming so soon after Switzerland had gone 2-0 ahead, was the turning point.
"To end up drawing in the home country of football is very good but we don't want to overestimate it, we have to move on," said the German. "We had a lot of players unavailable, played a new system and midfielder Gokhan Inler was outstanding. He is an idol to the rest of the team.
"I am disappointed we didn't win after being 2-0 up but I will not reprimand the team. I was pleased with the result in the end," added Hitzfeld.
England have now gone four matches without a win at Wembley, their worst sequence at home for 30 years, and lacked a cutting edge up front without the suspended Wayne Rooney.
Although Bent worked hard, wingers Theo Walcott and James Milner failed to provide him with many chances.
When openings did come Bent's way in the second half, he failed to add to his run of scoring in his last three England matches.
The first was when he failed to beat Benaglio after being put through by a stunning past from Jack Wilshere. He then skied the ball over the bar with Benaglio on the ground after saving from Young.
Switzerland were disciplined and tight with Granit Xhaka, 18, having a fine debut and Barnetta ending a 32-match international sequence without a goal.
