Micanski is Kaisers' chief against young Reds
The Serbia forward, brought in on a free transfer from Standard Liege, played the first 45 minutes before he was withdrawn by manager Roy Hodgson.
By that time the Reds were behind, courtesy of Ilian Micanski's close-range tap-in.
Jovanovic was one of only two members of the squad who had played at the World Cup, the other being defender Sotirios Kyrgiakos who lasted 77 minutes.
The Greek almost made a perfect return to life in a Liverpool shirt as his second-minute through-ball put David Ngog in on goal but he dragged his shot wide.
Moments later the newly-promoted Bundesliga side replied with Slovakian Adam Nemec having a shot deflected just over.
The 19-year-old Liverpool reserve forward David Amoo then shot straight at Tobias Sippel and Martin Kelly had an effort deflected over from Jovanovic's corner before the hosts made the breakthrough.
In the 32nd minute Jiri Bilkey beat Daniel Ayala to the ball before crossing for Micanski to extravagantly flick home from six yards.
After the break the Germans created a couple of opportunities but Hodgson's youthful side - midfielder Lucas Leiva was the most experienced first-teamer - did not concede again.
Despite the defeat the result, and the goalless draw to Grasshoppers in midweek, will have given the Liverpool boss plenty of optimism as he embarks on his competitive Reds career with a Europa League third round qualifier against Macedonians FK Rabotnicki on Thursday without many of his first-team stars.
Aston Villa were beaten 2-1 by League of Ireland side Bohemians at Dalymount Park.
Conor Powell lobbed the ball in after a sliced clearance from keeper Brad Friedel to put the hosts ahead in the 20h minute.
Gabriel Agbonlahor and Stewart Downing both went close before the break, but it was substitute John Carew who finally levelled midway through the second half.
However, it was the Irishmen - knocked out of the Champions League qualifiers by Welsh minnows The New Saints - who finished stronger, and won it with 10 minutes left when Paddy Madden sent substitute Enzo clear.
Jermaine Beckford came off the bench to net a brace as Everton won 3-0 at Preston.
Chris Martin scored twice as Norwich beat Newcastle, promoted back to the top flight as Championship winners, 2-1 at Carrow Road.
Bolton had to settle for a 1-1 draw with League One side Rochdale.