Matthews, 23, was expected to challenge for the green jersey, but injuries suffered in a training crash this week have ruled the Australian sprinter out.
He has been replaced by 29-year-old Canadian rider Christian Meier.
"They are certainly very different riders. Michael is sprint orientated and Christian is not, but a super team mate. It changes our plans a little bit in aspects, but in other aspects it doesn't. The focus will be a little bit different," Orica-GreenEdge's sporting director Matt White told journalists.
The Tour de France begins today with a 190.5km stage from Leeds to Harrogate.