The Swiss team under new coach Vladimir Petkovic had several golden opportunities but could not translate them into goals.
Arsenal striker Danny Welbeck, meanwhile, scored both of England's goals, the first in the 58th minute and the second in the 94th minute.
"They (Switzerland) got better as the game went on but luckily we didn't deteriorate too much," England manager Roy Hodgson said after the game ended.
"We can do better," said Hodgson, a former coach of Switzerland.
England had been criticized for a lacklustre display in their 1-0 friendly victory over Norway last week, but with a new midfield diamond introduced by Hodgson, they put on an improved showing at St Jakob-Park.
Welbeck was deputising for the injured Daniel Sturridge and he rose to the occasion, touching home a cross from Raheem Sterling for his first goal and then sealing victory in stoppage time.
"I thought the way we approached the game from the first minute was exactly what we wanted, and we got our reward," Hodgson told ITV.
"We pressurised the ball well, but you need that first goal to get people to come out and attack you.
"From then I thought we looked dangerous and we had several chances to aggravate the scoreline before Danny Welbeck's second."
It was Switzerland's first competitive home defeat since a 3-1 loss to England in October 2010 and meant that new coach Petkovic began his tenure in losing fashion.
However, with the top two teams in the group guaranteed to qualify for the tournament in France, it is likely to prove a flesh wound for a side ranked ninth in the world after their run to the last 16 at the World Cup.
"We started the second half much better, with much more movement and speed, but we committed two major errors and conceded a goal," said Petkovic.
"It's a good lesson and we'll try to make up for it in the next game."
Facing the team he coached for almost four years, Hodgson used a diamond shape that saw Sterling line up behind Welbeck and Wayne Rooney, with Jordan Henderson, Jack Wilshere and Fabian Delph in midfield.
Delph was making his full debut and began brightly, but he was also booked after sliding in on Valon Behrami and Stephan Lichtsteiner in quick succession.