The $graphLookup aggregation stage allows for graph searches across unsharded collections or to use results from a sharded collection to perform a graph search in an unsharded collection. It does not allow for the "from" collection to be sharded.
We understand this is a painful and unfortunate limit on the capabilities of the query language. We strive to make it so that the distribution of data does not impact the experience with the database, but are unable to implement this improvement to our satisfaction at this time. Implementing this feature would be subject to the same problems as
SERVER-29159, where you can find a summary of the reasons we haven't implemented it. SERVER-29159 also describes some workarounds which may be applicable to your use case as well.
We plan to work towards this feature in the future, but have no specific target date or release at this time.