Carroll was dropped from the squad, and that sparked suggestion that he could get a full England call up, but that did not happen.
Stuart Pearce's men survived in the Municipal Stadium and their 2-1 first-leg win proved enough to book a spot at next summer's tournament in Denmark.
Daniel Sturridge wasted the visitors' best opportunity, while Marius Alexe missed a glorious chance for Romania as England held out.
Stuart Pearce: "On Friday we played extremely well; today we didn't play extremely well.
"What we did show was determination and it was a really gutsy performance, certainly from the goalkeeper.
"Right through the team, we showed guts and a few things were said at half-time in the dressing room, and the players took that on board.
"We showed some more spirit in the second half of the match and we're just pleased to be here."