Python 3.5, 87 bytes

import re
lambda s,p,r:re.sub('(.*?)'.join(p),'\g<%d>'.join(r)%(*range(1,len(r)),),s,1)

repl.it to verify all test cases.

How it works

• '(.*?)'.join(p) builds a search pattern that matches the subsequence to be replaced and anything between its elements.

  Since the modifiers are lazy, each (.*?) will match as few characters as possible.

  For the pattern ghost, the constructed regex is g(.*?)h(.*?)o(.*?)s(.*?)t.

• '\g<%d>'.join(r)%(*range(1,len(r)),) builds the replacement string, using string formatting.

  Each \g<n> refers to the n^th captured group, just like \n would.

  For the replacement 12345, the constructed string is 1\g<1>2\g<2>3\g<3>4\g<4>5.

• re.sub(...,...,s,1) performs at most one replacement in the string s.

Python 3.5, 87 bytes

import re
lambda s,p,r:re.sub('(.*?)'.join(p),'\g<%d>'.join(r)%(*range(1,len(r)),),s,1)

repl.it to verify all test cases.

How it works

• '(.*?)'.join(p) builds a search pattern that matches the subsequence to be replaced and anything between its elements.

  Since the quantifiers are lazy, each (.*?) will match as few characters as possible.

  For the pattern ghost, the constructed regex is g(.*?)h(.*?)o(.*?)s(.*?)t.

• '\g<%d>'.join(r)%(*range(1,len(r)),) builds the replacement string, using string formatting.

  Each \g<n> refers to the n^th captured group, just like \n would.

  For the replacement 12345, the constructed string is 1\g<1>2\g<2>3\g<3>4\g<4>5.

• re.sub(...,...,s,1) performs at most one replacement in the string s.

Python 3.5, 87 bytes

import re
lambda s,p,r:re.sub('(.*?)'.join(p),'\g<%d>'.join(r)%(*range(1,len(r)),),s,1)

repl.it to verify all test cases.

Python 3.5, 87 bytes

import re
lambda s,p,r:re.sub('(.*?)'.join(p),'\g<%d>'.join(r)%(*range(1,len(r)),),s,1)

repl.it to verify all test cases.

How it works

• '(.*?)'.join(p) builds a search pattern that matches the subsequence to be replaced and anything between its elements.

  Since the modifiers are lazy, each (.*?) will match as few characters as possible.

  For the pattern ghost, the constructed regex is g(.*?)h(.*?)o(.*?)s(.*?)t.

• '\g<%d>'.join(r)%(*range(1,len(r)),) builds the replacement string, using string formatting.

  Each \g<n> refers to the n^th captured group, just like \n would.

  For the replacement 12345, the constructed string is 1\g<1>2\g<2>3\g<3>4\g<4>5.

• re.sub(...,...,s,1) performs at most one replacement in the string s.

Python 3.5, 87 bytes

import re
lambda s,p,r:re.sub('(.*?)'.join(p),'\g<%d>'.join(r)%(*range(1,len(r)),),s,1)

Python 3.5, 87 bytes

import re
lambda s,p,r:re.sub('(.*?)'.join(p),'\g<%d>'.join(r)%(*range(1,len(r)),),s,1)

repl.it to verify all test cases.