Chelsea are into the quarterfinals after the extra-time win, which was suspended for almost two hours on 85 minutes due to local thunderstorms.
Reece James struck first for Chelsea, but after the game's resumption, Benfica drew level through an injury-time penalty.
In extra-time, after Gianluca Prestianni was sent off, Chelsea struck three quickfire goals through Christopher Nkunku, Pedro Neto and Kiernan Dewsbury-Hall to win the tie 4-1.
Colwill reflected to the Chelsea website: "It was a crazy game, to be honest. I think we were in control but then we went in for the storm break and we were just waiting and waiting. But we knew what we had to do: we had to come out and win.
"We knew they were going to come back out with energy, and they had time to have a team talk and get themselves started again. We came back out, and I thought we were doing well, keeping the ball and creating chances.
"Then the referee gave a free-kick and they got the penalty and were back in it. But we kept on going.
"We are winners, we had no choice but to win that game. We all believed in that, even when they scored. Our heads didn’t drop and we continued to create chances. Now we move on to the next one."