According to the official Ethereum 2.0 Validator FAQ, the beacon chain mints fresh ETH as rewards by updating the balance of each PoS validator after every epoch:
How are rewards/penalties issued?
Remember that each validator has its own balance – with the initial balance outlined in the deposit contract.
This balance is updated periodically by the Ethereum network rules as the validator carries (or fails to carry) out his or her responsibilities.
Put another way, rewards and penalties are reflected in the validator’s balance over time.
In Phase 0, the beacon chain will not support public transactions - just PoS messages - so there will be no transactions from which to earn transaction fees. During Phase 1.5 when the Ethereum 1.0 chain is rolled into 2.0, transaction fees will come into play, though something like eip-1559 might burn the majority of them.
Epochs last about six and a half minutes, and validator balances are recalculated after every epoch:
How often are rewards/penalties issued?
Approximately every six and a half minutes – a period of time known as an epoch.
Every epoch, the network measures the actions of each validator and issues rewards or penalties appropriately.
So to answer your question directly, the Ethereum 2.0 protocol mints new ETH by increasing the ETH balances of live, honest validators every six and a half minutes. That new issuance goes directly into the validator client accounts, the validators being owned by the stakers.