It is possible to generate a RFC3161 timestamp token with Bouncycastle libraries.
First create a TimestampRequest. For your case it is only a wrapper for the digest algorithm and the digest value.
byte[] document = /* ... */
byte[] digest = MessageDigest.getInstance("SHA256").digest(document);
TimeStampRequestGenerator tsReqGen = new TimeStampRequestGenerator();
TimeStampRequest tsReq = tsReqGen.generate(CMSAlgorithm.SHA256, digest);
Then generate the token
DigestCalculator dgCalc = new JcaDigestCalculatorProviderBuilder().build();
ContentSigner signer = new JcaContentSignerBuilder().build(getPrivateKey());
SignerInfoGenerator siGen = new JcaSignerInfoGeneratorBuilder(new JcaDigestCalculatorProviderBuilder()).build(signer, getCertificate());
ASN1ObjectIdentifier policy = new ASN1ObjectIdentifier("1.2.3.4.5.6"); // Replace by your timestamping policy OID
TimeStampTokenGenerator tstGen = new TimeStampTokenGenerator(siGen, dgCalc, policy);
/* Set the parameters e.g. set the accuracy or include the signing certificate */
TimeStampToken tst = tstGen.generate(tsReq, generateSerialNumber(), new Date());
byte[] encoding = tst.getEncoded();