Henin and the third seeded Kuznetsova had begun their match on Saturday but play was suspended with the Belgian top seed serving at 2-3 in the deciding set as darkness fell over the Steffi Graf Stadium.
Henin, who begins the defence of her French Open title at the end of the month, served her seventh double fault of the match to gift Kuznetsova a match point at 4-5 and then put a backhand wide to see her hopes of a fourth Berlin title dashed.
Henin told a news conference it had been a very demanding week in Berlin, with numerous interruptions for rain and poor light, blustery conditions and slippery courts.
"It was very dangerous actually and everyone was scared they were going to get injured," she told reporters.
"I had a lot of difficult moments but I just kept fighting."
DECIDING SET
Kuznetsova, the world number four and a former U.S. Open champion, had only beaten Henin once in 15 previous meetings.
She served for the match at 5-3 in the second set on Saturday but Henin clung on to force a deciding set. The Belgian had come back from the brink of defeat earlier on Saturday to beat Serbia's Jelena Jankovic in their delayed quarter-final.
Ivanovic, 19, reached her first final on clay on Saturday when unseeded Ukrainian Julia Vakulenko withdrew from their semi-final because of a hand injury with the Serb leading 4-3.
Kuznetsova has never played Ivanovic on clay but has won both their previous meetings, including a straight-sets victory on the hard court at Sydney last year.
If the Russian wins in Berlin, it would be her first title on clay in five years.
The French Open, where Henin has won three of her five grand slam titles, begins at Roland Garros in Paris on May 27.
Henin said on Sunday she would be taking two weeks off to rest and train and would miss next week's event in Rome.
"I'm glad because I had a good preparation here and a lot of matches on the clay and that's good for the French," she said.
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