The secretary of state has approved the Silvertown tunnel, linking the Greenwich Peninsula in the Royal Borough of Greenwich with the Blackwall Tunnel approach road in London Borough of Newham.
The decision was made using a Development Consent Order under the Nationally Significant Infrastructure Project regime, following an examination by inspectors which finished in April last year.
The secretary of state approved the scheme, after concluding that it would address a need to reduced congestion on the existing approach to the Blackwall Tunnel.
He also said that, although emissions from vehicles using the tunnel may result in a worsening in air quality in some areas, the scheme would "not impact on the mayor’s wider aspirations of improving air quality in London as set out in his draft public consultation London environment strategy published in August 2017".
Last year, a decision on the application was postponed by ministers for a second time 'to enable further consideration of the effect of the scheme on air quality'.
Welcoming the decision, mayor of London Sadiq Khan, said: "New river crossings are vital for the future prosperity of east London, and the scheme will have a substantial impact in unlocking new jobs and economic growth, while easing congestion and poor air quality in the area."
The design of the new 1.4km tunnel is intended to allow for the introduction of user charging and accommodation of large vehicles, including double decker buses.
The decision to approve the application was criticised by campaigners against the new road link.
No to Silvertown Tunnel chair Anne Robbins said: "We are disappointed, but we are proud to have spoken up for communities on both sides of the Thames who objected to having more traffic imposed on them.
"We still believe that this will ultimately make the congestion problem worse, by adding to traffic jams elsewhere.
"The environmental mitigation suggested – such as running a cycle bus through the tunnel – is a hollow joke, while tolls will just punish those who need to use the tunnel."
The newly-elected mayor of Newham, Rokhsana Fiaz, added her voice to those opposing the tunnel.
She said: "The tunnel will also attract extra traffic into to the borough, leading to increases in noise and congestion for our residents, especially those living in the south of the borough."
But David Leam, infrastructure director at business body London First, said "The existing crossing at Blackwall is a notorious congestion blackspot that can cause traffic paralysis across south east London.
"Silvertown is an essential part of TfL's plans to improve public transport in east London and vital to keeping the whole city moving."
Separately, the London Borough of Greenwich's overview & scrutiny call-In sub-committee voted last night to ask the authority's director for regeneration, enterprise and skills, to renegotiate a proposed legal agreement covering a package of tunnel-related benefits with Transport for London.