What happens when the index size of my Mysql instance exceeds the innodb_buffer_pool_size?
It isn't the index size... it's the data and indexes.  The InnoDB Buffer Pool:

...holds cached InnoDB data for both tables and indexes
— http://dev.mysql.com/doc/refman/5.6/en/glossary.html#glos_buffer_pool
The larger the buffer pool, the more InnoDB acts like an in-memory database, reading data from disk once and then accessing the data from memory during subsequent reads. The buffer pool even caches data changed by insert and update operations, so that disk writes can be grouped together for better performance.
— http://dev.mysql.com/doc/refman/5.6/en/innodb-buffer-pool.html

Conversely, the smaller the buffer pool, the less InnoDB acts like an in-memory database.
In an ideal world, your buffer pool is larger than data size plus index size plus a little bit of overhead, because InnoDB does nothing to a page from a tablespace without storing that page in the buffer pool, it follows that when the pool is full, something less recently used gets evicted from the pool.  Practicality, of course, often necessitates something smaller than the ideal, and the key to appropriate sizing is the working data set.  The more infrequently-accessed data you have on your server, the fewer potential performance issues you should expect from an undersized pool.
There is, of course, no formula for this... familiarity with your unique working data set is the only &quot;tool&quot; you can use... but SHOW STATUS LIKE '%buffer%'; will give you the counters.
Note that Innodb_buffer_pool_pages_free is only an indication of completely unused space in the pool... it's not an emergency situation or even intensely meaningful if this value is very low or 0, because there is no process to spontaneously evict pages from the pool even when they are old and idle... but as long as they aren't &quot;dirty&quot; then replacing one page with something else is essentially no different in cost than loading a page into free space.  Zero free only means that at some point since the server was started, the total data and indexes read into the pool exceeded the size of the pool and there have not been enough deletions or tables dropped since the last peak to free up any pages.  Note also that running a backup will tend to fill an undersized pool, relatively harmlessly, depending on what's been loaded into the pool by the prior workload.