Both sides started the match fairly tentatively, cancelling each other out for much of the first half until the hosts started to force the issue, coming close through Grant Leadbitter and Tommy Smith.
Middlesbrough could have broken the deadlock four minutes into the second half, but substitute Lukas Jutkiewicz put his shot wide from just three yards out.
Instead, it was Boro who punished Ipswich for not being clinical enough when, just minutes after the missed penalty, Hoyte found Jutkiewicz, who made no mistake this time.
The Tractor Boys finally found an equaliser five minutes before the end through Leadbitter, making up for his earlier penalty miss.
The result means that Ipswich remain 15th in the Championship table, while Middlesbrough stay in fifth position.