Stevenage ended Leyton Orient's long unbeaten run to secure a home Vertu Trophy quarter-final tie against League One leaders Birmingham City.
Orient, who were eighth in League One before Tuesday's three league fixtures, had not been beaten in 12 games before losing to a Stevenage side that has amassed seven fewer points in the third tier this term.
The only goal came midway through the first half when a corner from the right bounced into the net off Orient defender Brandon Cooper.
The hosts almost equalised in the 11th minute of second-half stoppage time, but Jordan Brown's effort from just outside the box hit the crossbar.
The quarter-final line-up will be completed on 4 February when Port Vale face Wrexham in the remaining last-16 tie.
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