The summer overhaul of Bayern's squad bore spectacular fruit a fortnight ago in a 7-2 thrashing of Spurs as winger Serge Gnabry scored four second-half goals.
"The 7-2 was a great match, a statement, but nothing more," insisted Bayern head coach Kovac after last season's finalists were routed.
Now Bayern must back up the Spurs trouncing in Athens on the back of below-par performances in the Bundesliga and the loss of Germany centre-back Suele.
Bayern suffered their first defeat this season 10 days ago by crashing 2-1 at home to Hoffenheim, then leaked a 91st-minute equaliser in Saturday's 2-2 draw at Augsburg to stay third in the Bundesliga.
The point at Augsburg carried a high price as torn knee ligaments means Suele should be sidelined for the next six months.
"We didn't pass the character test," admitted Gnabry after the Augsburg draw.
"We didn't put our chances away at the end, if we had converted one, it would have been all over. That's how we blew it.
"Sometimes you have games like against Tottenham where everything runs smoothly -- then you have days like today or against Hoffenheim.
"We simply have to do better with our chances."
Gnabry scored in Augsburg as did Robert Lewandowski who equalled the Bundesliga record with goals in each of the first eight games this season.
With 16 goals in 12 games in all competitions so far, Lewandowski is in the form of his career, but the 31-year-old is running out of time to win the Champions League trophy with Bayern.
His pre-season demands for reinforcements were answered with Ivan Perisic, 30, signed from Juventus and Philippe Countinho, 27, opted for Munich to reboot his career after an unhappy spell at Barcelona.
Countinho's silky passing provides Lewandowski with plenty of chances and the pair have forged a key partnership at the heart of Bayern's attack in the wake of Kovac's squad clean out.
Senior veterans Franck Ribery, 36, Arjen Robben, 35, and Rafinha, 34, who helped win the 2013 Champions League title, have all been moved on.
Despite having only recently turned 30, club stalwart Thomas Mueller has also been deemed surplus to requirements, starting on the bench in Bayern's last seven games as Countinho's back-up.
Mats Hummels has been sold back to former club Borussia Dortmund, but now his former centre-back partner Boateng can prove himself after Suele's injury.
Having been heavily linked to Paris Saint-Germain and Juventus this year, Boateng could now partner Lucas Hernandez at Olympiakos, where Bayern chase a third straight win to stay top of Group B.
Kovac had been using Suele, 24, and Hernandez, 23, as centre-backs, backed up by France's 2018 World Cup winner Benjamin Pavard, 23, who can play in the middle of defence or left-back.
Suele had been part of a key quartet of rising Germany stars at Bayern, along with Gnabry, Joshua Kimmich and Leon Goretzka -- all still only 24.
Bayern have reached at least the semi-finals of the Champions League in seven of the previous ten seasons, but crashed out in the last 16 to eventual winners Liverpool in 2018/19.
However, the effect of bringing in new blood like Countinho was obvious at Tottenham, where the ruthless performance suggested "Bayern are one of the favourites this season," said Sky pundit Didi Hamann.
Yet as the Hoffenheim and Augsburg performances showed, Kovac's new-look Bayern is still raw as the club looks to avoid another knock-out phase exit, like in recent years, against such teams as Liverpool, Real Madrid and Barcelona.
"A lot needs to go wrong for the other teams and everything must be perfect for Bayern to shorten the gap on the international stage," ex-Germany midfielder Stefan Effenberg told magazine Kicker.
"I see Barcelona, Liverpool, Manchester City and Juventus being ahead of Bayern."