Laurene-Danielle Jackson died in hospital on 6 November after being caught in a crush of people trying to leave Lava & Ignite on 18 October.
The coroner said the silence would be held in her memory.
Nabila Nanfuka died at Northampton General Hospital on 19 October 2011.
An inquest into their deaths is currently being held at the County Hall in Northampton.
Jurors have heard how more than 900 students had bussed into Northampton from universities around the country - including Nottingham, London and Luton.
They were joined by another 700 or so on the door, taking the club to around capacity.
The inquest has heard how a DJ on the night made 14 announcements in 30 minutes telling club goers that their coaches were leaving which led to a crowd of people forming near the cloakroom.
CCTV footage showed hundreds of people emerging from the dance floor and onto the stair case to try to leave the venue.
No criminal charges have been brought against anyone following the crush.
Ms Nanfuka, 22, from Neasden in north London, was studying a leisure and tourism degree at the University of Northampton.
Ms Jackson, 19, from Wembley, was studying psychology at Kingston University.
Both were found unconscious in the club, and died as a result of asphyxia sustained in the crush.
The inquest is set to continue for another two weeks.
The inquest into deaths of two students killed as they tried to leave a nightclub in 2011 is to observe a minute's silence on the anniversary of one of their deaths.