More than 2,000 police and soldiers threw a security cordon around Sucre in a bid to stop demonstrators blocking Congress.
But senate leader Hormando Vaca Diez suspended the emergency session after security could not be guaranteed.
One Congressman said some legislators fled after the violence erupted, while Mr Vaca Diez was reportedly rushed under military protection to an unidentified army base.
Rumours that Mr Vaca Diez was seeking to flee Sucre caused protesters to march towards the airport to prevent his airplane from departing.
Tens of thousands of protesters, seeking greater distribution of the country’s gas wealth, have marched over the past weeks and prevented Congress from meeting in La Paz, forcing lawmakers to relocate to Sucre.
Coro Mayta, a union leader, was shot as he and scores of other militant miners tried to overwhelm an army checkpoint in the small town of Yotala, just outside Sucre.
According to the military, the protesters hurled sticks of dynamite as they attacked the checkpoint.
Bolivia has seen more than three weeks of violent protests over demands for the nationalisation of the natural gas industry and autonomy from its eastern provinces.
In a further development, the Bolivian military has warned it was ready to act against any attempt at secession within the country.
Calling for calm, Admiral Luis Aranda said the armed forces “will act if necessary to preserve stability and national sovereignty, the rule of law and the defence of democracy”.
President Mesa – who offered his resignation on Tuesday – has called on Mr Vaca Diez, who is first in line to succeed him, and the head of the Chamber of Deputies, Mario Cossio, to step aside to facilitate early presidential elections.
If both did so, it would allow Supreme Court Chief Justice Eduardo Rodriguez to become interim leader and call early elections.
Bolivia’s unrest has pitted poorer Andean regions around La Paz against the relatively prosperous eastern and southern plains, where most of the natural gas wealth is located.