Rooney was substituted during United's Premier League win over Liverpool last Saturday with a knee injury which required stitches.
However, scans showed no serious damage and United manager Alex Ferguson confirmed the England international would be available for the second leg of the last-16 tie at Old Trafford. United won the first match 1-0.
"Wayne is fine. We have a couple of doubts, but Wayne is not one of them," Ferguson told reporters.
United are without Ole Gunnar Solskjaer until the end of the month after he underwent minor knee surgery last week.
Ferguson's attacking options will be further depleted by the return to Sweden of Helsingborg striker Henrik Larsson, whose loan spell expires on March 12 following United's FA Cup quarter-final at Middlesbrough on Saturday.
