League One Stevenage knocked out Championship side Doncaster with a 3-2 win at the Keepmoat Stadium.
But Darius Charles made it 3-1 before Liam Wakefield's late consolation.
Coventry were another League One side to beat Championship opposition as they beat Barnsley 2-1 at Oakwell.
Jim O'Brien had put the Tykes ahead but Franck Moussa and Leon Clarke hit back for the Sky Blues with late goals.
Championship strugglers Millwall, last year's semi-finalists, were hammered 4-1 at League Two Southend.
Barry Corr's header put Southend ahead before Jermaine Easter was sent off for the Lions on the stroke of half-time, with Will Atkinson finding time to double the hosts lead before the interval.
Michael Timlin made it 3-0 before Martyn Woolford pulled one back, but Ryan Leonard had the last word.