The election took an uneasy turn on Tuesday when the opposition alleged that results were not being posted outside one-fifth of polling stations as required by law.
The Zimbabwe Electoral Commission (ZEC) says it will announce the final presidential results on Thursday evening.
Is there a peaceful way forward for Zimbabwe?
"Violence can not be part of that process", it added.
The government has accused the MDC of inciting Wednesday's unrest and vowed to enforce a security clampdown.
Before the police stormed the MDC headquarters, secretary-general Douglas Mwonzora said 27 party workers carrying out voter tabulation were locked inside its offices as police sealed them off on Thursday.
Mr Chamisa, opposition politician Tendai Biti and several others are suspected of the crimes of possession of risky weapons and public violence, according to a search warrant. The evidence already had been moved to a "safe house", he said.
In Harare, the contrast could not have been starker with November, when hundreds of thousands filled the streets, hugging soldiers and celebrating their role in ousting Mugabe, the only leader Zimbabwe had known since independence in 1980.
Mr Mnangagwa said the government was in talks with Mr Chamisa to defuse the crisis and proposed an independent investigation to bring those who were behind the violence to justice.
With Government championing new investment under the mantra "Zimbabwe is open for business", several worldwide investors have already starting coming to the country including from the West, which previously had a frosty relationship with the previous dispensation led by for president Mr Robert Mugabe.
A credible election after past votes were marred by violence against the opposition and alleged irregularities is crucial for the lifting of global sanctions and for the badly needed foreign investment to help Zimbabwe's long-collapsed economy revive.
The military deployment was the first time that soldiers had appeared in the streets of the capital since Mugabe's resignation.
The 94-year-old former president Mugabe, who ruled the country for 38 years, was pushed out of office by the country's military in November 2017. "We don't deserve the death we saw".