The Ivorian striker has netted 12 goals in 19 games in all competitions for Boro since joining in October on a short-term deal which ran until January.
Zoko arrived as a free agent having seen his contract with Notts County terminated by mutual consent in August.
Stevenage will now be hoping the 30-year-old can continue his goalscoring efforts over the second half of the campaign as they look to drag themselves off the foot of the table.
Boro have also revealed they have rejected bids from two unnamed League One rivals for highly-regarded midfielder Luke Freeman
Chairman Phil Wallace told the club's official website: "We are delighted to have retained Francois and to be able to turn down bids for Luke which we feel do not accurately reflect his talent.
"The recent FA Cup success has provided some additional finances which, while going nowhere near to addressing the financial shortfall of 2013, have certainly helped us make these footballing decisions."