How long do MNCs in India keep rejected job applications?

There is no standard rule for this. Each MNC will have its own set of rules. Some companies may keep the applications in their active file if they find somebody good and not able to accommodate the vacancy they are having at that moment. Once they get a suitable post, they will call the candidate again for interaction and may offer a job.
Many companies keep a record of candidates they rejected for a period of 2 years. Some may mention in their advertisement itself that candidates who applied for any post in the last year need not apply again.
Some companies will take only freshers and they may not consider the candidates who passed the examination more than one year before.
It all depends on the policy of that particular organisation. So they are is no harm in applying again. You may receive a call.

There is no uniform rule how long your application will remain in force for the consideration of MNC. Keeping mum of the employer, might give a signal that our applications might have been rejected but in the practical situations, it might not be like that.
Once there is the demand of the said post, the employer starts its process by calling the aspirants for the future interview. The best way to come out from such indecisive phase is to interact with the personnel department of MNC to assess the status of our applications.In some companies they maintain a panel of keeping of applications for nearly two years. In case of fresh advertisements, they remind their aspirants that the need not apply again if they have responded earlier.
Everything rests upon the policy of the company and nothing concrete can be established from our end regarding the regulations of the companies. Hence there is no harm to make a call, if we fill up the eligibility criterias.

The companies are getting a large number of job applications and it does not make any sense for them to keep them for a long time once the selection is made. Generally they will keep a few records pertaining to top candidates just in case the selected people did not join and they have to call the next line of merit. For an example if they have four vacancies then they could keep the record of top say 12 people only and in case the joining turn out is poor they would ask the next ones to take up the job. Generally the filling of the posts formalities are over within the three months of the selection process and then there will be a fresh advertisement for the remaining posts or new posts.
Another point is people nowadays go on adding skills through acquiring certificate and diploma courses and their qualifications go on increasing and accordingly their CVs would reflect those things and it is imperative that a fresh application is to be made in such cases.