Justice P D Naik gave Jacob three weeks' time to approach the court concerned in Delhi for relief.
The court in its order noted the applicant (Jacob) isa permanent resident of Mumbai and the FIR is lodged in Delhi, and the relief sought by her now is only temporary.
''The applicant apprehends that she will be arrested at any point of time. She has to make arrangements to seek relief from a court in another state. Hence, this court is of the opinion that protection as sought by the applicant can be granted for a temporary period,'' Justice Naik said.
The HC said since Jacob would be approaching the court concerned in Delhi to seek anticipatory bail, it would not be appropriate for this court to make any observations on merits of the case.
''The applicant is granted transit anticipatory bail for a period of three weeks to enable her to approach the court concerned in Delhi,'' Justice Naik said.
The court said if Jacob is arrested in the three-week period, then she shall be released after furnishing a bond of Rs 25,000.
Justice Naik also took note of the fact that another suspect in the case, Shantanu Muluk, an engineer based in Maharashtra's Beed district, was granted transit anticipatory bail for 10 days by the HC's Aurangabad bench on Tuesday.
Jacob and Muluk, who claim to be environmental activists, had approached the Bombay HC after a Delhi court issued non-bailable warrants against them.
According to the Delhi police, the two along with arrested accused Disha Ravi, an activist from Bengaluru, were allegedly involved in preparing the document and were indirect touch with ''pro-Khalistani elements''.
The Delhi police on Monday alleged that Ravi along with Jacob and Shantanu created the toolkit and shared it with others to tarnish India's image.
The accused persons have been booked under Indian Penal Code Sections 124(a) for sedition, 153(a) for promoting enmity between different sections of the society and 120(b)for criminal conspiracy.
Jacob's plea was opposed by the Delhi police's cyber cell which sought dismissal of the same.
Advocate Hiten Venegavkar, appearing for the Delhi police, on Tuesday argued that this court does not have the jurisdiction to grant any relief as the FIR is lodged in another state.
He further said when the Delhi police team searched Jacob's house on February 11, they had informed her that they would be questioning her further on February 12.
''However, Jacob went absconding since then. Due to this, the Delhi court issued a non-bailable warrant,''Venegavkar said.
He claimed Jacob and Disha Ravi had authored and created the toolkit document, which gave detailed directions on how the protest should be carried out, and it was made much before the January 26 ''riot'' incident at the Red Fort in Delhi.
Senior counsel Mihir Desai, appearing for Jacob, had argued that the toolkit was prepared by a number of people in support of the farmers and does not talk about violence or the Red Fort incident.
Desai said Jacob apprehended arrest, which was fortified by the issuance of a non-bailable warrant, and hence, left her house on February 12 and moved this court seeking transit anticipatory bail.
Jacob and Muluk in their pleas said they were targets of political vendetta.
Greta Thunberg, a celebrated climate activist, had shared the ''toolkit'' to lend support to the farmers' agitation near Delhi borders against the Union government's new agri laws.