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Did you followed fastuniq help

$ fastuniq
-i : The input file list of paired FSATQ sequence files [FILE IN]
Maximum 1000 pairs

This parameter is used to specify a list of paired sequence files in
FASTQ format as input, in which two adjacent files with reads in the
same order belong to a pair.

-t : Output sequence format [q/f/p]
q : FASTQ format into TWO output files
f : FASTA format into TWO output files
p : FASTA format into ONE output file
default = q

This parameter is used to specify sequence format in output file(s).
FastUniq could output read pairs into two files in either FASTQ [q]
or FASTA [f] format, in which reads in the same order belonging to a
pair. FastUniq could also output read pairs into a single file in
FASTA format [p], in which adjacent reads belonging to a pair.

-o : The first output file [FILE OUT]

-p : The second output file [FILE OUT]
Optional. ONLY required when output sequence format(-t) is specify as
[q] or [f].

-c : Types of sequence descriptions for output [0/1]
0 : The raw descriptions
1 : New serial numbers assigned by FastUniq
default = 0 

Thanks but it does not accept both fastq files

Ok ! 

fastuniq accept the name of fastq as a listfile. Create a listfile.txt and write both of your PE file name there, and call it with -i listfile.txt