The language was unveiled as Turkey's government faces international scrutiny for its crackdown on widespread protests, but the stance is in line with the long-held views of Merkel's party.
The program approved Sunday calls for deepening relations between Ankara and the EU and for "close strategic cooperation" on foreign and security policy.
"However, we reject full membership for Turkey because it does not fulfill the conditions for EU accession," it says. "In view of the country's size and economic structure, the European Union also would be overburdened."
Merkel has in the past talked of seeking a vaguely defined "privileged partnership" with Ankara, but the brief passage on Turkey in her Christian Democrats' manifesto didn't mention the term.
"We have learned that Turkey doesn't want it," Merkel told reporters. "So we described our aims differently."
Merkel governs in a coalition with a party that is less skeptical toward Turkey's bid, as are all her other conceivable coalition partners after the Sept. 22 parliamentary vote.
Her government supports continuing Ankara's membership talks, though Germany and the Netherlands last week blocked a decision to open a new chapter in those talks.
That contributed to tensions between Berlin and Ankara, which spiked over recent days after Merkel criticized Turkey's crackdown on demonstrations.
The protests in Turkey erupted three weeks ago after riot police brutally cracked down on environmental activists opposing plans to develop Istanbul's Gezi Park.
The demonstrations soon turned into expressions of discontent against Turkish Prime Minister Recep Tayyip Erdogan. The premier's critics say he is showing increasingly authoritarian tendencies, something he denies.
On Friday, Germany summoned Turkey's ambassador over a Turkish minister's suggestion that Merkel was picking on Ankara for domestic political gain. Turkey then said it was summoning Germany's ambassador.
The two countries' foreign ministers met Saturday in an effort to calm matters.