"I think it will not be as good as it [has] been when it has a good strong ally," he told reporters in Johannesburg
"Having a weaker ally is not good for the ANC."
Mantashe said the expulsion of the National Union of Metalworkers of SA (Numsa) was bad for the Congress of SA Trade Unions, the ANC, the alliance and society.
However, he said the ANC could not tell Cosatu to reverse the expulsion.
Read: Mantashe: Numsa expulsion overall bad
Numsa was expelled from Cosatu during a special central executive committee meeting which ran into the early hours of Saturday morning.
During the meeting Numsa presented its argument to Cosatu on why it should not be expelled, but this did not stop its ousting by 33 votes to 24.
Numsa has been at loggerheads with Cosatu since its general secretary Zwelinzima Vavi was suspended last year for having an affair with a junior employee. She originally claimed he had raped her but did not press charges with the police. Numsa took Cosatu to court to reverse the suspension, where it won its bid and Vavi returned to work.
Numsa held a special national congress in December where it resolved not to support its traditional ally the ANC in the general elections.
Cosatu charged Numsa with contravening its constitution.
An ANC task team, led by party deputy president Cyril Ramaphosa, intervened earlier this year to help Cosatu deal with internal friction.
Read: Mantashe: ANC cannot impose solutions on Cosatu
Mantashe said the ANC made its recommendations, but these were not binding on the union federation.
The team met all Cosatu affiliates and the national office bearers and made recommendations pertaining to the unity of Cosatu.
"We are in the alliance as independent parties. We don't dictate to another alliance partner what to do."
The ANC would engage with Cosatu and express its view that it was a bad idea.
"It's up to the federation itself to wake up and smell the coffee and reverse their decision," he said.
The parties involved needed to be ready to swallow their pride.
Mantashe was adamant the ANC had not failed in its intervention.
"If they reject unity I don't think we can call it our failure.
"If the federation... rejects unity it can't be the failure of the ANC it is the failure of the federation to appreciate the importance of unity," he said.
Read: More unions quit Cosatu's exec body
Earlier on Monday, seven unions supporting Numsa and calling for its expulsion to be reversed said it was suspending its participation from the Cosatu CEC until it had received mandates from their members.
The unions also said they would continue to call for a special national congress, a call Numsa had been making before its expulsion. This was rejected by the Cosatu leadership.
Mantashe said a special national congress should not be used to fight factional battles.
"The worse thing you can do to yourself is go to a special congress to fight it out.
He said it would be self-destructive.The objective of a special national congress should be to discuss the issues and have an objective of rebuilding unity in the trade union federation.
Read Fin24's live updates of the ANC addressing the media on Numsa's expulsion from Cosatu.
Allowing a split in the Federation can only help the historic enemies of the Alliance from both the left & right of the political spectrum— ANC Info Feed (@MyANC_) November 10, 2014