A 2-2 draw at Wembley on Thursday consigned Spurs to a 3-2 aggregate defeat and brought their European campaign to an end for this season.
Eriksen opened the scoring after only 10 minutes but Harry Kane scored an own goal and Dele Alli was sent off before half-time, leaving the home side with a mountain to climb at Wembley.
Spurs dominated play after the break but could not complete the turnaround after Victor Wanyama's fine goal on 61 minutes, and Jeremy Perbet's late strike on the break ensured Gent's place in Friday's last-16 draw.
"We are very disappointed with what we did today and over two games against Gent," Eriksen told BT Sport.
"They did not have a shot in the first half but still got a goal. We gave it away after getting in front. We weren't good enough in our finishing or our final pass.
"Overall, we did what we could. The referee was not on our side either. Even with 10 men we had chances to get the winner. We can blame the ref but we had our chances and we weren't good enough."
6 - Spurs have conceded more goals in four European games at Wembley this season (6) than in 12 league games at White Hart Lane (5). Curse.— OptaJoe (@OptaJoe) February 23, 2017
Gent boss Hein Vanhaezebrouck felt his side actually produced a comparatively poor performance but was nonetheless thrilled with a moment of "history" for the Belgian club.
"It was tough. This might be just about the worst European game in my time," he said, as quoted by Het Nieuwsblad.
"We escaped a few times because they were much better.
"All in all, this is fantastic - a performance for the history books. But I would have preferred to see better football."
Thomas Foket admitted that matters became tough after Wanyama's strike but praised his team-mates for their fighting spirit.
"After the 2-1, it was really difficult. They might have had 10 men, but they're still Tottenham," he said.
"How we fought just isn't normal. The team spirit prevailed."