The winning design features arches that are similar to the architecture of the Basilica as well as the National Shrine of the Immaculate Conception, where the papal Mass will be held, opposite the university campus.
It was chosen from the 18 entries by students showing off a range of designs according to The Washington Times.
Matthew Hoffman from Pittsburgh is one of the winners, he said: "Having our client be the pope really kept us driving through the whole process."
Mr Hoffman and his teammates, Ariadne Cerritelli of Bethesda, Maryland, and Joseph Taylor of Eldersburg, Maryland said their altar aims "to bring focus not on itself, but on the Vicar of Christ himself, who can preach from it."
Six delegates from the university, the basilica and the Archdiocese of Washington examined the submissions before deciding on first place, which included a $6,000 (almost £4,000) prize.
Cardinal Donald Wuerl, the Archbishop of Washington, said at the awards ceremony: "The creativity, beauty and thought that went into each of the submitted designs is a visible sign of God's grace at work among us in a unique way."
He added what an "incredible task" the teams faced in having just two weeks to design an altar, chair and pulpit that will remain in the basilica "for generations and generations to see."
University President John Garvey said students other than architecture students also submitted designs: "This was truly an interdisciplinary effort.
"Every school here has an important role to play in the life of the Church [and] making beautiful things is a way to find our way to God."
At the Mass, the Pope is expected canonize Junipero Serra, a Spanish Franciscan friar who established the first nine of 21 missions in California during the 18th century.
