The French Guianan jungle will resonate to an unexpected noise on Thursday – the deep-throated blast of a Russian space rocket as it soars into the morning sky. The Soyuz launcher will be making its first flight outside the former Soviet Union, carrying two European navigation satellites into orbit.

The mission marks a major shift in thawing relations between the two powers. Success for the launch will also bring considerable relief to the 350 Russian engineers and technicians who have grafted for four years to carve a £500m launch site out of the sticky rainforest on the coast of France's outpost in Guiana. Malaria and yellow fever are endemic here and building of Russia's Sinnamary site has been a colossal undertaking. A half-mile railway has been installed along with a special gantry to house rockets and satellites, protecting them from the equatorial humidity and heavy rain.

The stakes are high, Russian and European space officials admit, because they want Soyuz, the most dependable space rocket ever built, to be used to ferry humans into space in a few years' time.

"Now that we are about to launch our first Soyuz, we have begun looking at the idea of flying humans into space from French Guiana," said Patrick Loire, vice-president of Arianespace, which runs the main spaceport. "We are definitely thinking about it, though we haven't got a mission in mind yet."

The new launch site uses exactly the same techniques that Russia has perfected over the past 50 years. Soyuz's three stages are put together horizontally and then the whole vehicle is raised to the vertical by four huge metal arms that will hold it in place until just before launch.

Power will be switched to the rocket's internal batteries and at 11.34am UK time its engines are scheduled for ignition. A vast fiery plume will shoot into the 28-metre-deep flame trench that has been carved below the launchpad as the rocket, it is hoped, rises above French Guiana.

The creation of Russia's Sinnamary launch site – built just north of the Kourou base used by Europe's workhorse launcher, the Ariane 5 – has been an extraordinary endeavour involving hundreds of engineers. In effect, a replica of Russia's Baikonur base has been built on the edge of the Amazon.

To reach the complex involves a drive deep into the Amazon jungle along a road lined with mangrove swamps, thickets of palm trees and endless security posts. The main station is surrounded by a tall, electrified fence and coils of barbed wire.

Fuel dumps, stores and administration buildings dot the site. In the main integration building – where launchers are put together after being shipped from Russia – technicians have already put together the second Sozuz scheduled to lift off from the site on 16 December, carrying two French Earth observation satellites.

It may seem an extraordinary venture – the interplanetary equivalent of Fitzcarraldo's plans to build an opera house in the Amazonian jungle – but the benefits of a launch site here are straightforward. Guiana lies on the northern Atlantic coast of South America between 2 and 4 degrees north, and launching rockets from a site near the equator brings enormous advantages. Earth's rotational speed is greatest at the equator and so gives launchers a kick into space, reducing fuel use. Hence Russia's desire to build a launch site in French Guiana in order to complement its existing cosmodromes at Baikonur in Kazahkstan and Plestesk in Russia, both at relatively high northerly latitudes.

In addition, Soyuz has put more satellites into orbit than any other rocket on the planet. Early versions put Sputnik and Yuri Gagarin into orbit. Russia, with its European partners, expects to find a whole new market for its operations as a result, one of these being the launch of European astronauts and Russian cosmonauts from the unlikely starting point of this Amazonian rainforest space centre.

European space scientists – who have provided the home for the new Russian launch site – will also be watching the liftoff anxiously. Soyuz's double cargo will form the basis of Galileo, a new satellite navigation system that will free Europe from reliance on America's GPS satellites.

The creation of this multi-satellite project has been mired in controversy since its inception. Spiralling component costs and technical problems have seen the costs of Galileo – which is backed by the European Commission – soaring from €1.8bn to more than €5bn, cash that has been provided entirely by Europe's taxpayers. The project has also infuriated American defence officials, who claimed it would help their enemies direct attacks on the US and who once threatened to blow Galileo satellites out of the sky if they felt it necessary.

Feelings have calmed in recent years. Nevertheless, for both Europe and Russia a great deal is riding on today's launch. "No one here is talking about the possibility of failure," said one Esa official. "This is a very big mission."

Galileo will free European business from reliance on America's GPS system. The new system – which will be made up of more than 30 satellites orbiting at 23,000 kilometres – was expected to have been operational a year ago but ran into a maze of technical and political obstacles and came very close to being abandoned in 2007. In the end, the public-private partnership that had been put in place to build and run the project collapsed and EU member states had to agree to fund the entire project from the public purse.

In addition, the ability to launch satellites on Soyuz rockets will provide both Russia and Europe with a new tool for their joint space endeavours. Europe's Ariane 5 and Vega rockets represent the heaviest and lightest launchers on the market. Soyuz will give it a medium-lift launcher of incredible reliability. Almost 2,000 Soyuz have been blasted into space over the past 50 years, with very few failures.

It will be a track record that both space powers hope will be maintained on Thursday.

• This article was amended on 19 October 2011. The original stated that French Guiana is a French colony. This has been corrected.