Filipe de Jesus Corona-Verbera was convicted of drug-smuggling charges, for being the in-house architect for the highly violent Guzman drug-trafficking organisation.
Among his other exploits he had designed a series of secret rooms in buildings and warehouses used to store currency, drugs and weapons.
The 52-year-old architect had been on the run for 13 years before being arrested in the US in 2003.
The tunnel - which was discovered in 1990 - was designed with a hugely complex hidden entrance.
A tap was turned on outside a Mexican house on the border that caused a section of concrete flooring under a pool-table inside to rise 2.5 metres into the air through the use of hydraulic pumps.
The shaft then dropped 10 metres to the tunnel, which extended 61 metres under the border and came up through a false drain into a warehouse on the other side.
The extraordinary structure was revealed to police after more than 900kg of cocaine was found to have made its way into the States through the tunnel.
'The guilty verdict is the result of many years' hard work by prosecutors in the US attorney's offices,' Paul K Charlton, the prosecutor, said after the conviction.