Rooney, who pulled level with Bobby Charlton's 45-year-old mark of 49 goals when he scored with a penalty against San Marino on Saturday, again made no mistake from the spot when he thundered the ball past Swiss keeper Yann Sommer after Granit Xhaka had fouled Raheem Sterling.
Harry Kane, who came on as a 57th-minute substitute broke the deadlock with a well-taken left-foot shot after 67 minutes of a largely drab encounter.
England, who qualified for next year's finals in France after beating San Marino 6-0, preserved their 100 percent record in the group to move on to 24 points from eight successive wins.
With two matches remaining Switzerland have 15 points and Slovenia, who beat Estonia 1-0, have 12.
Apart from Rooney's historic goal, and Kane's earlier strike, there will be little to remember from a flat dull game which had the feel of a pre-season friendly, especially in the first half.
Switzerland, who could have secured their own place in the finals with a victory if the match between Slovenia and Estonia ended in a draw, were just as lacklustre as England for long periods.
Although they did play with slightly more ambition than the hosts, at least until they fell behind, they rarely troubled England goalkeeper Joe Hart.
The atmosphere at Wembley became more and more subdued as the pace and tempo of the game dropped, and the only time there was any hint of excitement was when Rooney looked like having an attempt at goal.
The second half was not much more exciting although both teams did at least have some attempts at scoring.
Swiss midfielder Xhaka forced Hart to push the ball away for a corner with a close-range header, while at the other end Rooney tested Sommer with a header and a long-range shot that he fired straight at the keeper.
Kane pepped up the England attack when he replaced midfielder Jonjo Shelvey after 57 minutes and he then produced a rare moment of quality when he swept home with his left foot for his third goal for England in his four appearances 10 minutes later.
It was left to Rooney to have the last word and he finally found the net to rewrite England's record books.
(Reporting by Mike Collett; editing by Toby Davis)
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