After impressing by taking five for 32 in the first fixture in Colombo last week, Wood has been sent home because of a side injury.
Something similar ended his season in the match against Yorkshire at Scarborough in late August last year and after being named in the England Performance squad he was sent to Loughborough for strength and conditioning work.
It will be a worry for Durham that the Ashington paceman has broken down again six weeks ahead of their trip to Abu Dhabi for the MCC v Champions match.
National Selector James Whitaker said: "Mark had a very impressive start to the tour. However, having been injured, it is very important that he has every chance of starting the season for Durham in the best possible condition. We have agreed with Durham that the best course of action is for Mark to return home."
Onions has spent most of the winter in Durban, playing for the Dolphins, but has not enjoyed enormous success.
Whitaker added: "We have been monitoring his progress in South Africa, and now this presents him with a chance to impress ahead of the summer international series."
England Lions will play three four-day Test matches against Sri Lanka A in Kandy, Dambulla and Colombo.
Yorkshire pair Jonny Bairstow and Liam Plunkett both made hundreds as the final warm-up match against Sri Lanka A Emerging Players ended in a draw on Saturday.
Plunkett, whose only other first-class century was for Durham against the university three years ago, hit a career-best 114 as the Lions reached 289 for six declared in their second innings. The Emerging Players were set 464 to win and finished on 177 for four, Durham's Scott Borthwick failing to add to the four for 25 he took in the first innings.
He was out-bowled on the final day by Lancashire's Simon Kerrigan, who had such a traumatic Test debut against Australia at the Oval last year. He had match figures of five for 81.
Plunkett, who made his Test debut at 20, feels his move to Yorkshire last season has refuelled his passion for the game.
"I am now 28 and last year I fell back in love with cricket," he said.
"After a couple of years that were a bit of a downer, I have been excited to play and I was looking forward to coming out to Sri Lanka with Yorkshire in three or four weeks. To come out a bit earlier is good fun."
He was not in the original squad but was called up when Sussex's Chris Jordan was added to the England Twenty20 squad in Australia, while Wood was a replacement for Somerset's Jamie Overton.
Another bowler who had to drop out through injury was Northamptonshire's David Willey, who had been tipped for a place England's World T20 squad.