Jovic scored five minutes in to put Frankfurt 1-0 up on the night and in the tie, with Inter offering little of note in response as the Bundesliga side secured their place in the quarter-finals.
It would have been more for Frankfurt if not for Samir Handanovic's fine form, while Sebastien Haller also hit the bar and had a goal disallowed.
And Spalletti, whose side were without a recognised striker due to Lautaro Martinez's suspension and Mauro Icardi's continued absence, conceded Inter lacked the belief required to lodge a comeback.
"We lacked a bit of everything. We lost balance immediately and made some mistakes for the opener, then got irritable and lost even more balance," he told Sky Sport Italia.
"It became a very difficult game. If you don't clear your lines first, or make rough passes, everything becomes an open ball to challenge for. If you treat it with more quality, it's within your control.
"Even when moving the ball between spaces, we never created anything of note. The early goal just cranked up the tension and made us feel as if there was no chance. We lost it straight away.
"We had plenty of time to deal with the situation intelligently. Instead, we were immediately frenetic and chaotic, trying to force the ball through with individual moves rather than as a team."
Spalletti, however, has urged Inter's support to remain patient with their side despite seeing them fail in both the Champions League and Europa League this term.
"There are high expectations, we want to be a winning team straight away, but there's very little chance of that," he added.
"What we have to do is try to bring home some important results via balance, but we lost our balance immediately.
"We certainly need to do better than we did tonight. We need more confidence. We'll look back over this match and recognise we didn't read it the right way."