England have 10 points from their four matches, two more than Slovenia who won 1-0 in Malta on Friday.
Scotland's second successive 3-0 defeat leaves them fifth with four points after four games and poorly placed to qualify for a first major tournament since the 1998 World Cup.
"I feel really proud of the way they played and the way they went about their job," said Scotland manager Gordon Strachan after the game. “They've been tremendous for me. There are times when the game is just not fair. And what happened in the match was not fair.”
While Strachan’s position is becoming increasingly tenuous, the chances of Gareth Southgate becoming full-time England manager are improving.
The 46-year-old accepted the role as interim manager in September after Sam Allardyce was forced out of the England manager's job in the wake of a newspaper sting.
The victory against Scotland was the most convincing performance of a Southgate side following a laboured 2-0 win over Malta and a nervy 0-0 draw in Slovenia.
"I will enjoy the result,” Southgate said. “I was asked to take the job for four games and to keep the country top of the group," he told ITV after the match. “The match was important for the supporters and the team. It was important they came through a pressure game, especially at Wembley, " he added.
“I’ve enjoyed the responsibility and challenge of every part of the job and I know that’s not so enjoyable if you don’t get the results as well. It’s been a brilliant experience.