England's autumn is beginning to look as bleak as the Twickenham weather after Willem Alberts' fortunate try earned South Africa a 16-15 victory.

Stuart Lancaster's men now head into next weekend's appointment with world champions New Zealand on the back of narrow defeats at home to Australia and the Springboks.

England competed every step of the way with South Africa, matching the Springboks for intensity and desire and they battled back from 16-6 down with real heart. They were the better team, particularly in the second half when Owen Farrell came on, but their undoing was a slice of bad luck just after the interval.

When Ben Youngs' hacked clearance rebounded off JP Pietersen, the ball fell to Alberts who scored rugby's equivalent of an open goal.

Farrell added three penalties to the two struck by Toby Flood as England battled all the way to the death. Lancaster will be encouraged by those qualities. But assistant coach Graham Rowntree himself said yesterday that he was sick of talking about lessons learned and England, despite Alberts' fortunate try, could have won the game.

Flood missed two first-half penalties and again the spotlight will fall on a decision made by captain Chris Robshaw when England were awarded a kickable penalty with just over a minute remaining.

Last week, England were criticised for not taking their points. Today, Robshaw instructed Farrell to go for goal when the lineout looked the better option. Farrell slotted the penalty, but England could not gather the restart and South Africa held on to extend their unbeaten run in this fixture to 11 matches, dating back to 2006.

England had drawn heart from their 14-14 draw with South Africa in the third Test of the summer tour. Those lessons Rowntree referred to included the need to match the Springbok physicality. Joe Launchbury was given his first international start while Alex Corbisiero, Tom Wood and Ben Morgan were brought back to bring some steel into the England pack. They all delivered. Youngs justified Lancaster's decision to promote him into the starting side with a clever display at scrum-half, as did Mike Brown on the wing.

England reprised their tour tactic of using two full-backs and the grim, wet conditions meant this was always going to be an arm-wrestle in the rain at Twickenham. England had to display their intent from the outset and did, with Geoff Parling blocking Ruan Pienaar's box kick and Robshaw pounced on Patrick Lambie to win the penalty.

Flood missed his shot at goal but England kept the pressure on as Brown claimed a confident high ball and escaped two defenders. Parling and Morgan both piled forward as England drove within five metres of the Springbok line. Chris Ashton was wrapped up but England won a second penalty shot at goal for offside and this time Flood made no mistake with the boot.

England defended resolutely when Flood lost the ball as he tried to run from deep but Eben Etzebeth stole a lineout and the Springboks earned a penalty which Lambie converted. Flood returned from a brief spell in the blood-bin to exchange penalties with Lambie but then missed a second penalty shot at goal, earned by a strong England scrum. Morgan crashed holes in the Springbok defensive line but England could not capitalise and Lambie edged the Springboks ahead for the first time in the match.

England came searing out of a scrappy passage of play, dominated by the boot and some poor kick-chasing, with a clean break from Alex Goode onto a clever ball from Ben Youngs. But Flood's kick in behind skipped dead in goal before Manu Tuilagi could get to it and England then wasted a five-on-three overlap. Just after the restart, South Africa extended their 9-6 half-time lead in a bizarre circumstances.

When Juande Kruger lost control as he drove for the line, Ben Youngs tried to hack the ball clear but it crashed into JP Pietersen. The ball rebounded towards Morgan, who could not gather it on his own line and Springboks flanker Alberts pounced to score a try that was converted by Lambie. Lancaster reacted to England falling 10 points down by sending on Farrell for Flood and they raised the intensity.

JP Pietersen could not take an excellent box-kick from Ben Youngs and Morgan spread the play wide for Tuilagi, who crashed through the South African defence. A mistake from Farrell put England on the back foot but they came storming out of defence with an interception from Tuilagi inside his own 22.

Tuilagi powered downfield and then fed Ashton but a poor pass to Brown, who should have come closer, checked England's momentum and a promising move ended when Launchbury knocked on. England kept piling on the pressure, helped by some poor South African kicking. Mako Vunipola crashed into the Springbok 22 and England won another penalty when Francois Louw came in off his feet.

Farrell converted it and then booted England back into South African territory but again the Twickenham crowd were left frustrated as Ashton knocked the ball forward. England came again and, with a minute remaining, earned the kickable penalty which Robshaw, eventually, instructed Farrell to kick for goal.