Recently I got the system which has MySQL server version 5.1 was running. It was good chance for me to reproduce the issue and show practical answer on question asked on stackoverflow.

Operating System: CentOS 6.5
Arch : x86_54

Symptom MySQL service failed to start after upgrading from MySQL 5.1 to 5.6 version.

Given below is the error found after upgrading to MySQL server version 5.6 from 5.1. You can get the below error in MySQL error log file.

2014-11-29 02:22:56 2175 [ERROR] InnoDB: auto-extending data file ./ibdata1 is of a different size 640 pages (rounded down to MB) than specified in the .cnf file: initial 768 pages, max 0 (relevant if non-zero) pages!
2014-11-29 02:22:56 2175 [ERROR] InnoDB: Could not open or create the system tablespace. If you tried to add new data files to the system tablespace, and it failed here, you should now edit innodb_data_file_path in my.cnf back to what it was, and remove the new ibdata files InnoDB created in this failed attempt. InnoDB only wrote those files full of zeros, but did not yet use them in any way. But be careful: do not remove old data files which contain your precious data!
2014-11-29 02:22:56 2175 [ERROR] Plugin ‘InnoDB’ init function returned error.
2014-11-29 02:22:56 2175 [ERROR] Plugin ‘InnoDB’ registration as a STORAGE ENGINE failed.
2014-11-29 02:22:56 2175 [ERROR] Unknown/unsupported storage engine: InnoDB
2014-11-29 02:22:56 2175 [ERROR] Aborting

Solution :

To solve this problem add the below given line in /etc/my.cnf file inside [mysqld] block.

innodb_data_file_path = ibdata1:10M:autoextend

Now restart the mysql service.

service mysqld restart

I hope the issue is resolved for you also.

Reference taken from MySQL knowledge base.