The witness said Jonathan directed Metuh to give Anenih N21m and N25m to a Presidential aide among others.
Metuh had allegedly collected the money from the former national security adviser (NSA), Sambo Dasuki.
The witness, Mr Richard Ihediwa, who was led in evidence by the Metuh's counsel, Mr Emeka Etiaba, told the Abuja High Court that Jonathan gave the directive on how the amount was to be spent.
According to him, N21 million was paid to former PDP Chairman, Chief Tony Anenih, for a property acquired for use by the party as its media intervention centre.
He said: "The amount covered the cost of hiring the structure, utility vehicles as well as security gadgets at the centre."
The witness also told the court that various sums were paid to some groups coordinated by some government functionaries, including the late Oronto Douglas and Abbah Dabo.
He said he was not very certain about the amount released to late Douglas, but added that N25 million was released to Dabo as mobilisation fee for advocacy groups, in line with the directive.
Ihediwa said the former president also approved different amounts for some other groups and Metuh disbursed the funds to them accordingly.
He said because of the tension and high level of insecurity across the six geo-political regions of the country then, there was the need for government to mobilise various advocacy groups to stabilise the system.
Justice Okon Abang has reserved ruling for November 15 on applications filed by the defence counsel.