The riverboat service, operated by Thames Clippers Logistics, will run daily at 7.30am.
The shipments will be loaded from electric vehicles onto the boat at Wandsworth Riverside Quarter Pier before travelling at high speed along the Thames to Bankside Pier for final mile delivery on DHL courier bicycles.
The service builds on DHL's experience in Venice where it has a well-established canal delivery network.
"With traffic and poor air quality becoming an increasing problem in urban areas like London, we're committed to finding a better blend of transport," said Ian Wilson, chief executive of DHL Express in the UK and Ireland.
"This new and unique service, combining electric vehicles, riverboat and last-mile bikes creates fast and efficient access across the capital."
Sean Collins of Thames Clippers Logistics said: "We're thrilled to be facilitating this service alongside DHL.
"The river is a widely under-used natural source of transportation and as we have demonstrated over the last 21 years with our passenger services, the river has opportunity to innovate and evolve - this new high-speed parcel delivery service is a great example of this.
"As a business we strive to maximise the uses of the river as a mode of transport and will continue to reduce congestion on London's roads."
Robin Mortimer, chief executive of the Port of London Authority, said: "This project opens up the movement of small parcels as a new and potentially substantial area of river use.
"The shipment of bulkier freight by river already takes more than 200,000 HGVs off the capital's roads every year.
"A river boat and emission free last mile delivery is a great innovation and the ideal combination for the city's next evolution."