Transport allowance is withdrawn by CBDT, i.e. provisions relating to exemption of ‘Transport Allowance’ of Rs. 1,600 pm for salaried individuals/ employees to meet their commuting costs between residence and office, stands withdrawn from 1 April, 2019 (FY 2018-19/ AY 2019-2020). It may be noted that reintroduction of Standard Deduction by the Finance Act, 2018 has resulted in getting transport allowance withdrawn.

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However, it may be noted that the Transport Allowance up to Rs. 3,200 pm shall continue to be exempt in the case of an employee, who is blind or deaf and dumb or orthopedically handicapped with a disability of lower extremities.  
Transport Allowance is withdrawn from AY 2019-20: CBDT Notification No. 17/2018 Income Tax dt. 6 April, 2018 As follows:-

MINISTRY OF FINANCE
(Department of Revenue)
(CENTRAL BOARD OF DIRECT TAXES)

                        NOTIFICATION

                 New Delhi, the 6th April, 2018

(Income-tax)

S.O. 1517(E).—In exercise of the powers conferred by section 295, read with sub-clause (ii) of clause (14) of section 10 of the Income-tax Act, 1961 (43 of 1961), the Central Board of Direct Taxes hereby makes the following rules further to amend the Income-tax Rules, 1962, namely:-
(1) Short title, Commencement and application.– These rules may be called the Income-tax (Third Amendment) Rules, 2018.
(2) They shall come into force on the 1st day of April, 2019 and shall apply to the assessment year 2019-2020 and subsequent assessment years.
2. In the Income-tax Rules, 1962, in rule 2BB, in sub-rule (2), in the Table, against serial number 10, the entries under columns (2) to (4) shall be omitted.
                                                            [Notification No. 17/2018/F. No.370142/02/2018-TPL]                                                                                                                Pravin Rawal.Dir.(TPL-II)                                                                            

Note : The principal rules were published in the Gazette of India vide notification No. S.O. 969(E), dated the 26th March, 1962, and was last amended by vide notification number G.S.R. 332(E) dated 03/04/2018.