The Nerazzurri fell 3-1 at Serie A leaders Juventus to drop to sixth place and pile further pressure on Mazzarri.
Reports in Italy claimed Inter were considering making a coaching change with Mazzarri, who joined the San Siro outfit last summer from Napoli, having won only eight of his 22 league games in charge and suffering a last-16 exit in the Coppa Italia.
However, Thohir has vehemently denied those rumours and in a statement on the club's official website said: "After the close of the January transfer window and the game in Turin, I feel it is appropriate for me to outline our sports strategy.
"We are going through a transition year and our main aim is to lay the foundations for our future: this is a difficult season and clearly it is not easy to find another winning combination like the one we had a few years ago.
"This is why we must be patient and move forward with a clear vision focusing on two basic concepts: how to improve our performance on the pitch and how to build our team for the future.
"To achieve the first target we have hired one of the best Italian coaches in circulation, Walter Mazzarri, with whom we are working for the present and planning for the future."
Inter strengthened their team in the winter transfer market with the arrivals of Italian full-back Danilo D'Ambrosio from Torino and Brazilian midfielder Hernanes from Lazio.
Thohir added: "The signings of Hernanes and D'Ambrosio - chosen by myself, our management and the coach in unison - are indicative in that sense: two key players who can help this club get going again. They will undoubtedly contribute greatly both this year and in the coming seasons.
"Regarding the future, it's important to stress that we have not yet taken any decisions about the players who currently make up our roster: the coach's assessment at the end of the Serie A season will be decisive in that respect. I will sit down and discuss with him which players possess the necessary qualities and motivation to remain with us, and which players are to make way for new faces.
"Of course this is not forgetting that we would all like to return to the European stage as soon as possible, and with our fans' support and passion we will start fighting again, from this Sunday, to achieve the best possible result this season."
Inter are 11 points adrift of Napoli, who are third and hold the last Champions League qualifying spot.
The Nerazzurri host Sassuolo on Sunday looking for their first win since beating AC Milan 1-0 on December 22.