Wanjiru, 24, won in London in 2009, but dropped out halfway last year through injury and has not raced since winning the Chicago Marathon last October.
The Kenyan, whose wife dropped attempted murder charges against him earlier this year, said: "I am bitterly disappointed not to be able to race in London this year. Winning the London Marathon in 2009 was one of the great achievements of my career and I was hoping to become the London champion again.
"But I have been suffering some problems with my right knee recently which meant I had to withdraw from the Lisbon half-marathon.
"Unfortunately, it has not responded well enough for me to make my final preparations for London. I wish good luck to the other runners and will do my best to be back next year."
Fellow Kenyan Lel won in London in 2005, 2007 and 2008 and, after two years of his own injury problems, now believes he is in shape to challenge for a fourth title.
Race director David Bedford said: "Of course we are very sad to lose the Olympic champion from our line-up as Sammy was a great champion here two years ago. We wish him a speedy recovery from his injury problems.
"But we are also delighted to announce the late addition of Martin Lel, one of the great champions in London Marathon history.
"Martin tells me his training has been going really well and he feels in shape to be able to take on the London challenge again. He is a very welcome addition to what is already a great field."