The court sentenced Chikumbeni Mwanatheu, 35, to two months in prison with hard labour after he admitted a charge of witchcraft, police spokesman Augustus Nkhwazi said.
Mwanatheu had pleaded guilty to a charge of "conduct likely to cause a breach of peace" after he boasted that he had prevented rain from falling on his neighbour's field, the spokesman said.
Magistrate Lameck Mkwapatira ruled he "needed to be given a custodial sentence to let the community enjoy peace in his absence and for his own safety."
The poor tobacco-producing southern African country has suffered drought since last year.
Belief in witchcraft and magic runs deep in Malawi. The practice is punishable by up to five years in prison and suspects are often killed by mobs.
Just R20 for the first month. Support independent journalism by subscribing to our digital news package. 