The bill authorizes SUNY's four-year colleges and universities to boost tuition by $300 annually for five years. That would raise tuition for full-time students to about $6,470 a year after five years, from under $5,000 now.
Tuition for students from outside the state would also increase 10 percent.
It allows SUNY's four research centers, including Stony Brook University, to add another $75 fee to tuition to help pay operating costs.
The plan also authorizes $140 million in capital spending at the research centers. Stony Brook has proposed using the funds to increase staff and expand a cancer research center.
Cuomo said a predictable rise in tuition was better for students and the universities than the way the state has managed tuition in the past: years of tuition freezes followed sometimes by increases as high as 40 percent.
"The political process has not handled setting tuition well," the freshman governor said. "Rational tuition is just what the word suggests: It's rational. Families can plan. Organizations can manage."
David Lavallee, provost of the SUNY system, said uncertainty about tuition levels too often has compelled some campuses to cut back on course offerings -- forcing students to take longer to graduate.
Stony Brook's president, Dr. Samuel L. Stanley Jr., called it a "historic day" for his campus and the SUNY system. He said the legislation will help "provide increased financial aid for our students, grow our faculty, improve research and patient care in cancer, and create new, high-paying jobs on Long Island."
Cuomo is expected to announce as early as next week the outcome of Stony Brook's grant application.