Sharepoint - Creating Lookup column using rest which can take multiple values

You can create lookup column from SchemaXml. For multi value lookup column, SchemaXml looks like

var lookupShema = "<Field Type=\"LookupMulti\" DisplayName=\"MultipleLookup\" Required=\"FALSE\" EnforceUniqueValues=\"FALSE\" List=\"{92a6545e-e509-430b-a6a6-16bdb7a81b33}\" ShowField=\"ID\" Mult=\"TRUE\" Sortable=\"FALSE\" UnlimitedLengthInDocumentLibrary=\"FALSE\" RelationshipDeleteBehavior=\"None\" ID=\"{32e8961d-d69f-448e-bf9a-f2246185d389}\" SourceID=\"{233ae45e-f581-4420-b069-b7a74d368b13}\" StaticName=\"MultipleLookup\" Name=\"MultipleLookup\" ColName=\"int3\" RowOrdinal=\"0\" Version=\"1\" /> "

See MSDN example for more details.

    $.ajax({
  url: "http://<site url>/_api/web/lists(guid'da58632f-faf0-4a78-8219-99c307747741')
    /fields",
  type: "POST",
  data: { '__metadata': { 'type': 'SP.Field' }, 'FieldTypeKind': 20, 'Title':
    'Stakeholders', 'SchemaXml': '<Field Type=\"UserMulti\" Required=\"TRUE\"
    UserSelectionMode=\"PeopleAndGroups\" UserSelectionScope=\"0\" Mult=\"TRUE\" />' },
  headers: { 
    "X-RequestDigest": <form digest value>,
    "accept": "application/json; odata=verbose",
    "content-type": "application/json;odata=verbose",
    "content-length": <length of body data>
  },
  success: successHandler,
  error: errorHandler
});

Add parameter 'AllowMultipleValues': true

Edit

To change lookup and enable allow multiple values You can refer same MSDN which Atish shared :

$.ajax({
  url: "http://<site url>/_api/web/lists(guid'da58632f-faf0-4a78-8219-99c307747741')
    /fields('1d22ea11-1e32-424e-89ab-9fedbadb6ce1')",
  type: "POST",
  data: "{ '__metadata': { 'type': 'SP.FieldLookup' }, 'AllowMultipleValues': true }",
  headers: { 
    "X-RequestDigest": <form digest value>,
    "content-type": "application/json;odata=verbose",
    "content-length": <length of body data>,
    "X-HTTP-Method": "MERGE"
  },
  success: successHandler,
  error: errorHandler
});