The 54-year-old was quick to praise his side's second-half display, but expressed concerns about how they dealt with long balls throughout.
"It was a victory achieved by our strength of will but the first half was bad," he told ZDF. During the second half and extra time we were the better team and had the better chances. We should have decided it during the second half.
"We gave away an awful lot of passes - this was unusual - and we had problems in getting behind their defenders.
"We had to switch our lineup again as Mats Hummels was not fit to play. Per Mertesacker and Jerome Boateng have played together many times and they know each other - normally they are very good. But Algeria played these long balls very well; they are very good at that."
Germany will take on France in the quarter-finals of the competition.