The Manchester United striker was absent from the 4-0 triumph over Newcastle on Saturday after picking up a knock in the first-leg 1-1 draw with the Bundesliga champions.
Scans, however, revealed no serious damage and the forward's return to light training over the weekend has boosted manager David Moyes's hopes of being able to call on his star striker at the Allianz Arena.
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"The manager and staff decided not to risk him against Newcastle in the hope that the extra few days would give him a better chance of being fit, and his chances are looking better than 70 percent at this stage."
Moyes told MUTV last week: "Wayne's got a badly bruised toe ... [and] it could be a problem for the Munich game on Wednesday. We need to monitor it. We'll get him treatment all over the weekend and see if we can speed it up."
That treatment looks to have worked, which will be a welcome boost to a United side already stripped of striker Robin van Persie because of a knee injury.
Rooney has 17 goals in all competitions this season and the England striker will likely need to be on top form if United is to knock out tournament favorite Bayern, which has an imperious record on home soil.
The Bavarians lost 1-0 at Augsburg over the weekend, ending an unbeaten streak that stretched an incredible 53 Bundesliga games, but are expected to make wholesale changes for the visit of United having rested a number of their stellar names at SGL-Arena.
Moyes' side faces an uphill battle to win through the last-eight clash, after Bayern midfielder Bastian Schweinsteiger's strike ensured the tie would be level at 1-1 going into the return meeting in Munich.