The treaty is a sign of support for Karimov, whose authoritarian rule has left his country increasingly isolated. Karimov welcomed the agreement.
"Today, we are reaching an unprecedented level in our relationship," Karimov said. "I understand and we all understand in Uzbekistan that it is unprecedented that Russia signs such a partnership agreement with Uzbekistan."
The treaty comes as Uzbekistan's Supreme Court today handed down guilty verdicts in the trials of 15 men accused of participating in the Andijon uprising last May.
Human-rights groups dismissed the trial as a show, saying much of the testimony may have been coerced.