“It was a very challenging campaign for us, but decisively we had a clear goal: we wanted to defend this state against a partly openly Right-wing extremist party,” Mr Woidke told broadcaster Tagesschau.
“We need to wait and see who can be in parliament [to form a coalition],” he added, referring to the Greens.
Kevin Kuhnert, SPD’s general secretary, said: “For us in the national SPD, when it goes well tonight the problems ahead of us don’t get bigger or smaller.
“We have a long process ahead of us if we want success in next year’s federal elections.”
The AfD, which had vowed “to send Woidke into retirement”, nonetheless hailed its strong showing, declaring it was the “strongest force in the east”.
Tino Chrupalla, the party co-leader, said it had “taken gold once and silver twice” in three elections in the east this month.
It is the third worst result for the CDU in post-war Germany’s history and its worst result in the east of the country.
A recent survey in the state found that immigration was the top concern for many voters.