The seventh-ranked Italian recovered from a shaky start to level against her Czech opponent but ended up sinking to a 6-2, 2-6, 6-4 defeat on Centre Court.
At Roland Garros last month she lost the final to world number one Iga Swiatek, winning just three games.
Despite the disappointments, it has been a remarkable rise for Paolini, the first Italian woman to reach a Wimbledon singles final.
The 28-year-old had never been beyond the second round of a Grand Slam before reaching the fourth round of the Australian Open earlier this year.
In the new rankings next week she will be number five in the world even though she ended last season down in 30th spot.
Paolini said she was still aiming at "great things" despite her painful losses in Paris and London.
"Sometimes I'm a little bit scared to dream too much," she said. "I have to say that. I don't know.
"I'm going back, trying to practise, to stay in the present, as I said many times. This is the goal for me, my team, to try to keep this level as much as possible.
"If I keep this level, I think I can have the chance to do great things."
She described her feelings as bittersweet.
"Today I was dreaming to hold the trophy, but it didn't go well," she said. "I'm just enjoying the position where I am right now, five in the world. It's unbelievable, honestly.
"I just did two finals in two Grand Slams. I have to be also happy with the results. Also a little bit disappointed."
